title: HEK293 TREX FLP-In hnRNPA1 Overexpression RNA-seq 2

city: Santa Cruz

first: Jonathan

middle: Michael

last: Howard

address: 1154 High Street

department: Molecular, Cell, and Developmental Biology

institute: University of California-Santa Cruz

description:
processed data file: cliptn_clipti_hg19.SE_minAD_0.33_minBF_5.0.miso_compare.txt
hekha1_clip_ti_jh46

data_processing:
iCLIP:  based on random bases of internal barcode positions 1-9 of each read, the readIDs were divided into classes (for later use in duplicate removal). Note: positions 4-7 comprised fixed values for each sample
iCLIP:  each read was searched for the presence of adaptor sequence TGGAATTC and trimmed from that point on. Reads without the adaptor were discarded. Reads shorter than 30bp after trimming (including internal barcode positions 1-9) were discarded.
iCLIP:  internal barcode positions 1-9 were trimmed before mapping
iCLIP:  reads mapping (by bowtie2) to human repeatMasker elements were discarded
iCLIP:  reads were mapped to hg19 by tophat, aided by a gtf file based on UCSC Knowngenes, and with parameters --no-novel-juncs, --no-coverage-search
iCLIP:  for each class of internal random barcode bases from step (1), duplicate read mappings of the same length and position were discarded
iCLIP:  peaks were called on the dup-removed bam files from step (6) by Clipper (Yeo et al) using default parameters for hg19.
RNAseq:  the 10^6x106bp pairedEnd reads were trimmed to 80x80 by trimming from each read, 5bp from the 5' end, 21bp from the 3' end
RNAseq:  reads mapping (by bowtie2) to human repeatMasker elements were discarded
RNAseq:  reads were mapped to hg19 by tophat, aided by a gtf file based on UCSC Knowngenes
RNAseq:  duplicate read mappings of the same start and end position were discarded
RNAseq:  bam files were filtered to extract read1 only (of the paired-end mappings) for input to MISO
RNAseq:  the dup-removed, read1 only, bam files were used as input to MISO (Katz et al, 2010) to determine the Percent-Splice-In (PSI) for the MISO-supplied hg19 SE (skipped exon) events
RNAseq:  miso-compare was run on the 4 pairwise comparisons of 2 tn (jh43, jh44) samples to 2 ti (jh45,jh46) samples.
RNAseq:  the miso-compare results were filtered for cases with a delta-psi absolute value at least 0.33 and a bayes-factor at least 5.0
RNAseq:  the 4 pairwise comparisons were merged into a single file, with columns indicating the presence or absence of minimum delta-psi and bayes factor for each comparison.
Genome_build: hg19
Supplementary_files_format_and_content: iCLIP-seq: gzip compressed bed file of Clipper peak calls with browser track line
Supplementary_files_format_and_content: cliptn_clipti_hg19.SE_minAD_0.33_minBF_5.0.miso_compare.txt For each pairwise comparison, there are columns for psi, delta-psi, and bayes-factor output from miso-compare. For each pairwise comparison, a column with value -1/0/+1 indicates delta-psi negative, not-called, or positive. The pairSum column is the sum of the -1/0/+1 values. The maxAbsDiff and maxDiffBf columns are the maximums, over the pairwise comparisons, of the abs(delta-psi) and bayes-factors

growth_protocol: For iCLIP and  RNA-seq, cells (control or T7-hnRNPA1 inducible) were grown in 10 cm2 cell culture plates reaching 70-80% confluency under tetracyclin treatment for 24 h, then harvested for downstrem application

extract_protocol:
For iCLIP protocol, nuclear extracts (detergent lysis) were prepared from  cells (control or T7-hnRNPA1 inducible)  prior to immunoprecipitation.  For RNA-seq, whole cell extracts (detergent lysis) were prepared from cells (control or T7-hnRNPA1 inducible)  and RNA was isolated using TRIreagentLS.
For iCLIP, libraries were constructed as previously described (Huppertz, I., et al. Methods. 2014) with minor changes. 3' Adenylated adapter, AIR ligase, and PCR primers used from NEXTflex™  Illumina Small RNA-Seq Library Prep Kit (Bioo Scientific) and RT primers were adapted for kit reagent use. For RNA-seq, and Panc1 RIP-seq,  NEXTflex™ Rapid Directional qRNA-Seq™ Kit was used (Bioo Scientific). For small RNA-seq library prepartation, NEXTflex™ Small RNA-Seq Kit v1 was used.
For iCLIP, RNA purification was performed as previously described (Huppertz, I., et al. Methods. 2014). For RNA-seq, PolyA+ selection was performed.

treatment_protocol: HEK293T TREX-FLP cells were selected with blasticidin (150µg/mL) and zeocyin at 75µg/mL (or hygromycin for induciblbe T7-hnRNPA1 cell lines at 150µg/mL) treatment at 150µg/mL for 3 days prior to use.

value: TREX FLP-In 293T cells

value: Epithelial

tag: tissue source

value: Human Embryonic Kidney

tag: overexpression

value: T7-tagged hnRNP A1

tag: molecule subtype

value: polyA+ RNA


title: hiPSC derived NPC_control_miRNA-seq 1

status: Public on Jun 01 2017

type: SRA

city: Buffalo

first: Michal

last: Stachowiak

state: NY

address: 3435 Main Street

department: Pathology and Anathomical Sciences

country: USA

institute: State University of New York at Buffalo

library_source: transcriptomic

data_processing:
CLC genomic workbench was utilized to align, and generate raw counts of microRNA
Alignment was done to miRNA database version 21
Genome_build: miRNA datavase version 21
Supplementary_files_format_and_content: Raw counts

molecule: total RNA

organism: Homo sapiens

source_name: hiPSC derived NPC_control

growth_protocol: hiPSC derived NPC were treated with neuronal media for 2 days (DMEM/F12, 1x N2, 1x B27-RA, 20 ng/ml BDNF, 20 ng/ml GDNF, 1mM dibuyryl -cyclic AMP, and 200nM ascorbic acid)

extract_protocol:
RNA was extracted using Qiagen Rneasy kit per manufacturor protocol
smallRNA libraries were prepared for sequencing using standard Illumina protocols

tag: source subject status

value: control; healthy

tag: cell type

value: iPSC derived NPC

tag: treated with

value: neuronal media for 2 days


title: hiPSC derived NPC_control_RNA-seq 4

data_processing:
Aligned to genome using Tophat2
Cufflinks was used to get expression profile
Cuffdiff was used for differntial expression
Genome_build: hg19
Supplementary_files_format_and_content: text file, genes expression levels in FPKM

extract_protocol:
RNA was extracted using Qiagen Rneasy kit per manufacturor protocol
RNA libraries were prepared for sequencing using standard Illumina protocols


title: hiPSC derived NPC_control_miRNA-seq 4


title: SRSF1_A1 overexpression iCLIP 1

state: CA

source_name: SRSF1_A1 overexpression iCLIP

tag: cell line

value: small RNA


title: SRSF1_control iCLIP 1

source_name: SRSF1_control iCLIP


title: SRSF1_A1 overexpression iCLIP 3


title: SRSF1_A1 overexpression iCLIP 2


title: Patient 3_NOTCH_ChIP-seq

library_source: genomic

data_processing:
Aligned using Bowtie2 to hg19 genome
peaks were called using MACS2 q=0.01
Genome_build: hg19
Supplementary_files_format_and_content: bed format contain peak locations

molecule: genomic DNA

source_name: hiPSC derived NPC_SCZD patient

extract_protocol:
lysate was sonicated and protein-genomic DNA complex were isolated with antibody
Libraries were prepared according to standard Illumina protocols

value: SCHIZOPHRENIA; SCZD

tag: chip antibody

value: NOTCH (obtained from Dr. Jon C. Aster)


title: Uninfected-1

city: Guangzhou

first: Yuqing

last: Li

address: North campus of Sun Yat-sen University, No.74 of Zhongshan 2nd road, Yuexiu Distinct, Guangzhou, Guangdong

country: China

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 and CQ994935.1 using bowtie software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with HTSeq v0.6.0.
Genome_build: hg19 and CQ994935.1
Supplementary_files_format_and_content: txt

source_name: Mesenchymal stem cell

growth_protocol: Human peridontal ligament stem cells (PDLSC) were cultured in alpha-MEM (containing 10% FBS and 1% anti-biotics).

extract_protocol:
After infection of KSHV for 48h and 96h, dicarded the supernatant, and total RNA from uninfected PDLSC, KSHV-48 and KSHV-96 were collected in triple, with Trizol reagent.
Library was constructed as following: Total RNA were enriched with beads binded with Oligo(DT), then broken into short fragments through fragmentation buffer. Broken RNA were used as template to synthetize the first- and second-strand of cDNA. Fragments in target size were recovered by Agarose gel electrophoresis, and amplified by PCR.

treatment_protocol: PDLSCs between passage 2 and 6 were infected with KSHV in MOI=50.

value: peridontal ligament cell

tag: passage

tag: tissue

value: peridontal ligament

tag: stress

value: uninfected


title: U2AF2_control iCLIP 2

source_name: U2AF2_control iCLIP


title: hiPSC derived NPC_control_RNA-seq 6


title: U2AF2_control iCLIP 1


title: U2AF2_A1 overexpression iCLIP 1

source_name: U2AF2_A1 overexpression iCLIP


title: SRSF1_control iCLIP 3


title: U2AF2_A1 overexpression iCLIP 3


title: U2AF2_control iCLIP 3


title: hnRNPA1_A1 overexpression iCLIP 2

source_name: hnRNPA1_A1 overexpression iCLIP


title: hnRNPA1_control iCLIP 1

source_name: hnRNPA1_control iCLIP


title: hnRNPA1_control iCLIP 2


title: 30 Gy cell 93

city: Hangzhou

first: Ling

last: Yang

address: 34th, Yanguan alley

institute: Hangzhou cancer institute

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C93_mapping.bam

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Repeated 12 Gy sequencing reads were combined. Then all reads were mapped to gencode v22 whole genome using tophat v2.0.14 with default parameters.
Reads count were calculated using Rsubread 1.2.0. The raw data was cleaned by scde package. The normalized number of reads count falling in the exons of this meta-transcript were generated by the DESeq2 package.
Genome_build: gencode v22
Supplementary_files_format_and_content: normalized reads counts for each sample

source_name: Esophageal squamous cell carcinoma

extract_protocol:
Cells were directly lysed and amplified with smart-seq2 kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Esophageal squamous cell carcinoma line KYSE-180

value: Esophagus

tag: irradiation

value: 30 Gy


title: HEK293 TREX FLP-In control RNA-seq 1

description:
processed data file: cliptn_clipti_hg19.SE_minAD_0.33_minBF_5.0.miso_compare.txt
hekha1_clip_tn_jh43

source_name: HEK293 TREX FLP-In control RNA-seq

value: TREX FLP-In 293T cells


title: U2AF2_A1 overexpression iCLIP 2

value: Epithelial


title: 30 Gy cell 91

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C91_mapping.bam


title: 30 Gy cell 88

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C88_mapping.bam


title: 30 Gy cell 92

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C92_mapping.bam


title: 30 Gy cell 89

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C89_mapping.bam


title: 30 Gy cell 87

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C87_mapping.bam


title: SRSF1_control iCLIP 2

value: Human Embryonic Kidney


title: HEK293 TREX FLP-In control RNA-seq 2

description:
processed data file: cliptn_clipti_hg19.SE_minAD_0.33_minBF_5.0.miso_compare.txt
hekha1_clip_tn_jh44


title: 30 Gy cell 86

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C86_mapping.bam


title: hnRNPA1_A1 overexpression iCLIP 1

value: T7-tagged hnRNP A1


title: HEK293 TREX FLP-In hnRNPA1 Overexpression RNA-seq 1

description:
processed data file: cliptn_clipti_hg19.SE_minAD_0.33_minBF_5.0.miso_compare.txt
hekha1_clip_ti_jh45

value: polyA+ RNA


title: 30 Gy cell 85

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C85_mapping.bam


title: 30 Gy cell 84

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C84_mapping.bam


title: 30 Gy cell 83

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C83_mapping.bam


title: 30 Gy cell 80

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C80_mapping.bam


title: 30 Gy cell 78

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C78_mapping.bam


title: 30 Gy cell 81

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C81_mapping.bam


title: 30 Gy cell 82

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C82_mapping.bam


title: 30 Gy cell 75

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C75_mapping.bam


title: 30 Gy cell 73

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C73_mapping.bam


title: 30 Gy cell 74

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C74_mapping.bam


title: 30 Gy cell 90

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C90_mapping.bam


title: 30 Gy cell 67

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C67_mapping.bam


title: 30 Gy cell 68

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C68_mapping.bam


title: 30 Gy cell 69

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C69_mapping.bam


title: 30 Gy cell 77

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C77_mapping.bam


title: 30 Gy cell 70

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C70_mapping.bam


title: 30 Gy cell 71

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C71_mapping.bam


title: 30 Gy cell 65

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C65_mapping.bam


title: 30 Gy cell 62

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C62_mapping.bam


title: 30 Gy cell 64

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C64_mapping.bam


title: 30 Gy cell 63

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C63_mapping.bam


title: 30 Gy cell 61

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C61_mapping.bam


title: 30 Gy cell 60

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C60_mapping.bam


title: 30 Gy cell 58

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C58_mapping.bam


title: 30 Gy cell 59

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C59_mapping.bam


title: 30 Gy cell 57

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C57_mapping.bam


title: 30 Gy cell 79

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C79_mapping.bam


title: 30 Gy cell 56

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C56_mapping.bam


title: 30 Gy cell 54

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C54_mapping.bam


title: 30 Gy cell 52

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C52_mapping.bam


title: 30 Gy cell 51

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C51_mapping.bam


title: 30 Gy cell 53

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C53_mapping.bam


title: 30 Gy cell 76

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C76_mapping.bam


title: 30 Gy cell 55

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C55_mapping.bam


title: 30 Gy cell 48

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C48_mapping.bam


title: 30 Gy cell 50

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C50_mapping.bam


title: 30 Gy cell 43

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C43_mapping.bam


title: 30 Gy cell 44

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C44_mapping.bam


title: 30 Gy cell 39

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C39_mapping.bam


title: 30 Gy cell 47

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C47_mapping.bam


title: 30 Gy cell 49

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C49_mapping.bam


title: 30 Gy cell 45

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C45_mapping.bam


title: 30 Gy cell 46

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C46_mapping.bam


title: 30 Gy cell 41

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C41_mapping.bam


title: 30 Gy cell 40

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C40_mapping.bam


title: 30 Gy cell 36

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C36_mapping.bam


title: 30 Gy cell 38

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C38_mapping.bam


title: 30 Gy cell 33

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C33_mapping.bam


title: 30 Gy cell 35

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C35_mapping.bam


title: 30 Gy cell 32

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C32_mapping.bam


title: 30 Gy cell 34

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C34_mapping.bam


title: 30 Gy cell 31

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C31_mapping.bam


title: 30 Gy cell 30

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C30_mapping.bam


title: 30 Gy cell 29

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C29_mapping.bam


title: 30 Gy cell 28

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C28_mapping.bam


title: 30 Gy cell 27

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C27_mapping.bam


title: 30 Gy cell 26

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C26_mapping.bam


title: 30 Gy cell 24

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C24_mapping.bam


title: 30 Gy cell 42

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C42_mapping.bam


title: 30 Gy cell 23

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C23_mapping.bam


title: 30 Gy cell 25

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C25_mapping.bam


title: 30 Gy cell 37

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C37_mapping.bam


title: 30 Gy cell 19

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C19_mapping.bam


title: 30 Gy cell 18

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C18_mapping.bam


title: 30 Gy cell 22

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C22_mapping.bam


title: 30 Gy cell 16

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C16_mapping.bam


title: 30 Gy cell 14

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C14_mapping.bam


title: 30 Gy cell 15

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C15_mapping.bam


title: 30 Gy cell 11

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C11_mapping.bam


title: 30 Gy cell 12

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C12_mapping.bam


title: 30 Gy cell 17

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C17_mapping.bam


title: 30 Gy cell 10

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C10_mapping.bam


title: 30 Gy cell 21

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C21_mapping.bam


title: 30 Gy cell 6

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C06_mapping.bam


title: 30 Gy cell 7

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C07_mapping.bam


title: 30 Gy cell 3

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C03_mapping.bam


title: 30 Gy cell 2

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C02_mapping.bam


title: 30 Gy cell 1

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C01_mapping.bam


title: 30 Gy cell 5

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C05_mapping.bam


title: 12 Gy rep2 cell 96

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H12_mapping.bam

value: 12 Gy


title: 30 Gy cell 4

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C04_mapping.bam


title: 12 Gy rep2 cell 95

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H11_mapping.bam


title: 12 Gy rep2 cell 94

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H10_mapping.bam


title: 12 Gy rep2 cell 93

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H9_mapping.bam


title: 12 Gy rep2 cell 92

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H8_mapping.bam


title: 30 Gy cell 20

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C20_mapping.bam


title: 12 Gy rep2 cell 91

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H7_mapping.bam


title: 12 Gy rep2 cell 90

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H6_mapping.bam


title: 12 Gy rep2 cell 88

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H4_mapping.bam


title: 12 Gy rep2 cell 89

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H5_mapping.bam


title: 12 Gy rep2 cell 87

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H3_mapping.bam


title: 12 Gy rep2 cell 85

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H1_mapping.bam


title: 30 Gy cell 9

description: Corresponds to Normalized_counts.txt column: Sample_Pan_B.C09_mapping.bam


title: 12 Gy rep2 cell 83

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G11_mapping.bam


title: 12 Gy rep2 cell 81

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G9_mapping.bam


title: 12 Gy rep2 cell 82

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G10_mapping.bam


title: 12 Gy rep2 cell 79

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G7_mapping.bam


title: 12 Gy rep2 cell 76

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G4_mapping.bam


title: 12 Gy rep2 cell 77

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G5_mapping.bam


title: 12 Gy rep2 cell 75

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G3_mapping.bam


title: 12 Gy rep2 cell 71

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F11_mapping.bam


title: 12 Gy rep2 cell 72

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F12_mapping.bam


title: 12 Gy rep2 cell 69

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F9_mapping.bam


title: 12 Gy rep2 cell 67

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F7_mapping.bam


title: 12 Gy rep2 cell 66

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F6_mapping.bam


title: 12 Gy rep2 cell 68

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F8_mapping.bam


title: 12 Gy rep2 cell 70

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F10_mapping.bam


title: 12 Gy rep2 cell 65

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F5_mapping.bam


title: 12 Gy rep2 cell 63

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F3_mapping.bam


title: 12 Gy rep2 cell 62

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F2_mapping.bam


title: 12 Gy rep2 cell 61

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F1_mapping.bam


title: 12 Gy rep2 cell 60

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E12_mapping.bam


title: 12 Gy rep2 cell 84

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G12_mapping.bam


title: 12 Gy rep2 cell 59

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E11_mapping.bam


title: 12 Gy rep2 cell 80

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G8_mapping.bam


title: 12 Gy rep2 cell 55

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E7_mapping.bam


title: 12 Gy rep2 cell 56

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E8_mapping.bam


title: 12 Gy rep2 cell 78

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G6_mapping.bam


title: 12 Gy rep2 cell 54

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E6_mapping.bam


title: 12 Gy rep2 cell 53

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E5_mapping.bam


title: 12 Gy rep2 cell 74

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G2_mapping.bam


title: 12 Gy rep2 cell 73

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G1_mapping.bam


title: 12 Gy rep2 cell 51

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E3_mapping.bam


title: 12 Gy rep2 cell 52

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E4_mapping.bam


title: 12 Gy rep2 cell 49

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E1_mapping.bam


title: 12 Gy rep2 cell 47

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D11_mapping.bam


title: 12 Gy rep2 cell 45

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D9_mapping.bam


title: 12 Gy rep2 cell 48

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D12_mapping.bam


title: 12 Gy rep2 cell 43

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D7_mapping.bam


title: 12 Gy rep2 cell 46

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D10_mapping.bam


title: 12 Gy rep2 cell 42

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D6_mapping.bam


title: 12 Gy rep2 cell 41

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D5_mapping.bam


title: 12 Gy rep2 cell 38

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D2_mapping.bam


title: 12 Gy rep2 cell 40

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D4_mapping.bam


title: 12 Gy rep2 cell 57

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E9_mapping.bam


title: 12 Gy rep2 cell 39

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D3_mapping.bam


title: 12 Gy rep2 cell 58

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E10_mapping.bam


title: 12 Gy rep2 cell 36

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C12_mapping.bam


title: 12 Gy rep2 cell 33

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C9_mapping.bam


title: 12 Gy rep2 cell 35

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C11_mapping.bam


title: 12 Gy rep2 cell 37

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D1_mapping.bam


title: 12 Gy rep2 cell 32

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C8_mapping.bam


title: 12 Gy rep2 cell 30

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C6_mapping.bam


title: 12 Gy rep2 cell 50

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E2_mapping.bam


title: 12 Gy rep2 cell 31

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C7_mapping.bam


title: 12 Gy rep2 cell 29

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C5_mapping.bam


title: 12 Gy rep2 cell 28

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C4_mapping.bam


title: 12 Gy rep2 cell 26

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C2_mapping.bam


title: 12 Gy rep2 cell 27

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C3_mapping.bam


title: 12 Gy rep2 cell 24

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B12_mapping.bam


title: 12 Gy rep2 cell 22

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B10_mapping.bam


title: 12 Gy rep2 cell 23

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B11_mapping.bam


title: 12 Gy rep2 cell 25

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C1_mapping.bam


title: 12 Gy rep2 cell 21

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B9_mapping.bam


title: 12 Gy rep2 cell 20

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B8_mapping.bam


title: 12 Gy rep2 cell 19

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B7_mapping.bam


title: 12 Gy rep2 cell 44

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D8_mapping.bam


title: 12 Gy rep2 cell 18

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B6_mapping.bam


title: 12 Gy rep2 cell 15

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B3_mapping.bam


title: 12 Gy rep2 cell 17

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B5_mapping.bam


title: 12 Gy rep2 cell 16

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B4_mapping.bam


title: 12 Gy rep2 cell 14

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B2_mapping.bam


title: 12 Gy rep2 cell 13

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B1_mapping.bam


title: 12 Gy rep2 cell 12

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A12_mapping.bam


title: 12 Gy rep2 cell 11

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A11_mapping.bam


title: 12 Gy rep2 cell 9

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A9_mapping.bam


title: 12 Gy rep2 cell 10

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A10_mapping.bam


title: 12 Gy rep2 cell 8

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A8_mapping.bam


title: 12 Gy rep2 cell 6

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A6_mapping.bam


title: 12 Gy rep2 cell 7

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A7_mapping.bam


title: 12 Gy rep2 cell 3

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A3_mapping.bam


title: 12 Gy rep1 cell 95

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H11_mapping.bam


title: 12 Gy rep1 cell 94

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H10_mapping.bam


title: 12 Gy rep2 cell 4

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A4_mapping.bam


title: 12 Gy rep2 cell 2

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A2_mapping.bam


title: 12 Gy rep1 cell 93

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H9_mapping.bam


title: 12 Gy rep1 cell 96

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H12_mapping.bam


title: 12 Gy rep1 cell 92

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H8_mapping.bam


title: PKM2_FLAG_HA_CLIP_rep1

city: Stanford

first: Gerald

last: Tiu

state: California

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University

description:
UV-crosslinked total RNA fragments
ribosome_profiling_CLIP_processed.csv
PKM2_FAST_iCLIP.bw

data_processing:
For RNA-Seq and Ribosome Profiling: For pre-processing, the 3’ adapter sequences (CTGTAGGCACCATCAAT) were removed using cutadapt (https://cutadapt.readthedocs.org/en/stable/). The 5’ end of each read was then removed using fastx_trimmer from FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
To remove reads that aligned to rRNA, tRNA, and snRNAs, reads were first aligned to rRNA, tRNA, and snRNAs using bowtie2 (bowtie2 parameters: -L 18) and aligned reads were subsequently discarded.
Filtered reads that did not align to rRNA/tRNA/snRNAs were then aligned to an mm9 transcriptome reference derived from UCSC knownCanonical using bowtie2 (bowtie2 parameters: --norc -L 18).
Ribo-Seq reads were then parsed for uniquely aligned reads and grouped by read lengths. In each length group, the distribution of distances of read 5’ ends to canonical translation start sites were assessed. The highest frequency distance plus an additional four nucleotides was then used to offset the 5’ end of each read to approximate the A site position of ribosome footprints based on prior analyses of ribosome footprint offsets from the A site. (<=28nt: A_position = start+4+9; 29-32nt: A_position = start+4+10; >=33nt: A_position=start+4+11)
RNA-Seq reads were also parsed for uniquely aligned reads and were assigned to particular nucleotide positions using the parameters determined for Ribo-Seq reads.
Ribo-Seq and RNA-Seq reads were then counted using 5’UTR, CDS, and 3’UTR annotations from UCSC mm9 knownCanonical.
To remove lowly expressing genes, genes with <150 reads in the CDS of any of the Ribo-Seq or RNA- Seq libraries were removed. Translational efficiency for each gene is defined as the library size normalized counts of Ribo-Seq reads aligning to the CDS (with the first 15 codons and last 5 codons removed) divided by library size normalized counts of RNA-Seq reads aligning to the CDS (with the first 15 codons and last 5 codons removed)
For FAST-iCLIP: Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the mouse (mm9) genome using bowtie2 (PMID: 25411354)
To compare ribosome profiling data to iCLIP data, Raw aligned iCLIP reads from the FAST-iCLIP analysis described above were then obtained prior to merging of RT stops from replicates. Each alignment was assigned to the 5’ end of each read. Alignments were counted using UCSC mm9 knownCanonical annotations. The counts over the total mature transcript, which includes the 5’UTR, CDS, and 3’UTR of each gene, for each replicate were calculated and averaged to obtain the mean CLIP read count for each gene. To calculate the enrichment of PKM2 iCLIP reads over RNA-Seq, a pseudocount of 1 was added to the mean iCLIP read count for each gene. The mean iCLIP read counts were then normalized to the total aligned library size. Normalized iCLIP counts were then divided by the library size normalized RNA-Seq counts from the control library to obtain the iCLIP enrichment score for each gene.
Further FAST-iCLIP processing (including RT stop identificaiton, gene assignment, and peak calling) for other analyses was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-Seq and Ribosome Profiling:  Also included are counts of reads aligning to 5UTR, CDS, and 3UTR of transcripts along with RPM (RNA-Seq, Ribo-Seq), translational efficiency (Ribo_RPM/RNA_RPM), iCLIP read counts, and RNA-normalized iCLIP enrichment values.

organism: Mus musculus

source_name: E14 mouse embryonic stem cells

growth_protocol: Mouse E14 embryonic stem cells (ESCs) were cultured on 0.1% gelatin-coated dishes using a serum-based medium, comprised of Knockout-DMEM (Life Technologies), 15% FBS (EMD Milipore), 2 mM non-essential amino acids, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol, and 105 U ml-1 LIF

extract_protocol:
For ribosome profiling experiments, extraction was performed as described before with modifications below (PMID: 22836135). Main modifications are the use of RNase A/T1 instead of RNase I for ribosome footprinting and the use of Ribo-Zero Gold rRNA removal kit. CHX-treated cells were lysed using polysome lysis buffer without SUPERase In RNAse Inhibitor (25 mM Tris-HCl, pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 8% glycerol, 1% Triton X-100, 0.5% sodium deoxycholate, 100 μg ml−1 CHX, 25 U ml-1 TurboDNAse (25 U ml-1 Ambion, cat. no. AM2238), Complete Protease Inhibitor EDTA-free (Sigma-Aldrich, cat. no. 11836170001), ProteCEASE EDTA-free (G biosciences, cat. no. 786-328) in nuclease-free water (Invitrogen)). RNA for RNA-Seq was isolated using TRIzol (Invitrogen) following manufacturer’s instructions. For ribosome profiling, after lysis, nuclei were removed by three consecutive centrifugations (1000g, 5 min at 4 °C). RNA amount is measured using UV spectrophotometry (Nanodrop ND-1000 spectrophotometer, ThermoScientific) and per ~ 600 μg RNA, 1 μg RNase A (Invitrogen, cat. no. AM2270) and 2000 U RNase T1 (Invitrogen, cat. no. AM2280) were used to footprint ribosomes for 30 minutes at RT. RNase A/T1 digestion was quenched with 180 U SUPERase In RNAse. Ribosomes were enriched by adding the RNAse digested lysate onto 1 M sucrose cushion in lysis buffer and centrifuged in a TLA100.3 rotor (Beckman) for 4 h at 70,000 rpm at 4 °C. The ribosome pellet containing the ribosome footprinted Ribo-Seq library was washed briefly in nuclease-free water and resuspended further in TRIzol (Invitrogen). For FAST-iCLIP, experiments were performed as described previously with the specific modifications below (PMID: 25411354). Whole-cell lysates were generated in iCLIP lysis buffer (50 mM HEPES, 200 mM NaCl, 1 mM EDTA, 10% glycerol, 0.1% NP-40, 0.2% Triton X-100, 0.5% N-lauroylsarcosine) and briefly sonicated using a probe- tip Branson sonicator to solubilize chromatin. Each iCLIP experiment was normalized for total protein amount, typically 1 mg, and partially digested with RNase I (ThermoFisher Scientific, cat. no. AM2294) for 10 min at 37°C and quenched on ice. PKM2-FLAG-HA was isolated with anti-FLAG agarose beads (Sigma-Aldrich) for 1 h at 4°C on rotation. Samples were washed sequentially in 1 ml for 5 min each at 4°C: 2× high stringency buffer (15 mM Tris-HCl, pH 7.5, 5 mM EDTA, 2.5 mM EGTA, 1% Triton X- 100, 1% sodium deoxycholate, 120 mM NaCl, 25 mM KCl), 1× high salt buffer (15 mM Tris-HCl pH 7.5, 5 mM EDTA, 2.5 mM EGTA, 1% Triton X-100, 1% sodium deoxycholate, 1 M NaCl), 1× NT2 36 buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM MgCl2, 0.05% NP-40). Purified PKM2-FLAG- HA was then eluted off anti-FLAG agarose beads using competitive FLAG peptide elution. Each sample was resuspended in 500 μl of FLAG elution buffer (50 mM Tris-HCl, pH 7.5, 250 mM NaCl, 0.5% NP- 40, 0.1% sodium deoxycholate, 0.5 mg ml−1 Flag peptide) and rotated at 4°C for 30 min. The Flag elution was repeated once for a total of 1 ml elution. PKM2-FLAG-HA was then captured using anti-HA agarose beads (Pierce) for 1 h at 4°C on rotation. Samples were then washed as previously in the anti- FLAG agarose beads.
For ribosome profiling experiments, library preparation steps were adapted from a previous protocol (PMID: 22836135) and the ARTseq Ribosome Profiling Kit manual (Epicentre, cat. no. RPHMR12126). After extraction and precipitation, both ribosome footprinting and RNA-Seq libraries were depleted of rRNA using the Ribo- Zero Gold rRNA Removal Kit (H/M/R) (Illumina, cat. no. MRZG126) following manufacturer’s instructions except that the 50 °C incubation step was omitted. Samples were then purified using Zymo Research RNA Clean and Concentrator-5 columns (Zymo Research, cat. no. R1016) as described in the ARTseq protocol. Libraries were then end repaired and ligated to linker as described previously (PMID: 22836135) with modified Zymo Research RNA Clean & Concentrator-5 column purification after each step (100 μl sample, 200 μl RNA Binding Buffer, 450 μl ethanol) instead of isopropanol precipitation. The RNA-Seq and Ribo-Seq libraries were sequenced on the Illumina NextSeq 500 with 75 bp single reads using the high output kit. For FAST-iCLIP experiments, preparation of UV-crosslinked material was prepared as per the FAST- iCLIP protocol (PMID: 25411354). Final library material was quantified on the BioAnalyzer High Sensitivity DNA chip (Agilent) and then sent for deep sequencing on the Illumina NextSeq machine for single-end 75-bp cycle run.
RNA-Seq, Ribo-Seq, iCLIP-Seq

treatment_protocol: For ribosome profiling experiments, E14 ESCs were transfected for 36 h with either 20 nM control or PKM1/2 targeting siRNAs using RNAimax (Invitrogen) following manufacturer’s instructions. Control and PKM knockdown ESCs were passaged 16 h prior to sucrose cushion purification. ESCs were treated with 100 μg ml-1 CHX for 2 minutes at 37 °C. For iCLIP experiments, PKM2-FLAG-HA cells were ultraviolet (UV) crosslinked to a total of 0.35 J cm−2.

tag: genotype

tag: sirna

tag: clip antibodies

value: anti-FLAG agarose beads (Sigma-Aldrich), anti-HA agarose beads (Pierce)


title: siPKM_RNA

description:
rRNA depleted total RNA
ribosome_profiling_CLIP_processed.csv

value: Wildtype

value: Dharmacon (ON-TARGETplus PKM Pool, cat. no. L-062711-00-0005)


title: PKM2_FLAG_HA_CLIP_rep2


title: siPKM_RPF

description:
Ribosome-Protected Fragments (RPFs)
ribosome_profiling_CLIP_processed.csv


title: 12 Gy rep1 cell 91

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H7_mapping.bam


title: 12 Gy rep2 cell 5

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A5_mapping.bam


title: Neutrophils from PBS livers-8

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7
FastQ files were indexed and mapped for Mm9 genome assembly using HISAT 0.1.5
SAM files were converted to BAM using SAMtools
BAM files were analyzed using Partek Genomics Suite 6.6 software (http://www. partek.com/pgs) and gene RPKM (Reads Per Kilobase of transcript per Million mapped reads) normalized reads were obtained.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes mRNA molecule count values for each Sample

source_name: Freshly isolated liver neutrophils

extract_protocol:
Mice were anesthetized and perfused livers were collected, cut into small fragments, and incubated with 5 mL digestion buffer composed by 5% Fetal Bovine Serum (FBS, Biological Industries, Israel), 0.5 mg/ml Collagenase VIII from Clostridium histolyticum (Sigma-Aldrich, USA), 0.1 mg/ml Deoxyribonuclease I from bovine pancreas (Sigma-Aldrich, USA) in Dulbecco’s Phosphate Buffered Saline with Calcium and Magnesium (PBS+/+, Biological Industries, Israel), in a shaker-incubator at 250 rpm, 37°C for 45 minutes. The samples were then subjected to three cycles of washing with PBS-/- at 400 rpm, 4°C for 5 minutes from which the supernatant was kept, omitting the parenchymal cell pellet. Subsequently, the supernatant was centrifuged at 1400 rpm, 4°C for 5 minutes and the cell pellet was lysed for erythrocytes by 2 minutes incubation with ACK buffer composed by 0.15 M NH4Cl, 0.01 M KHCO3, and washed with PBS-/-. For RNA-seq 50,000 neutrophil cells per liver were sorted by FACSAria directly into a 1.7 ml micro-tube containing 50 μl lysis buffer (RNase-free H2O, 0.2% Triton-X (Roth) and 0.4 U/μl RNasin (Promega). Antibodies used throughout the research are: CD11b (clone M1/70), Ly6C (clone HK1.4), Ly6G (clone 1A8),and CD45 (clone 30F11).
RNA-seq library production, sample preparation and analysis were carried out as previously described (Jaitin, D. A et al., Science 2014), using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science.
3' RNA-seq for digital gene expression quantitation

treatment_protocol:
FACS sorted cells
mice received an i.p injection of 400 µL anti-mouse CCR2 mAb (clone MC-21)-conditioned media (29 µg Ab/ml) or PBS-/-. The injections were performed, starting at 12 h prior to APAP challenge and every 24 h, till the time of sacrifice.

tag: strain

value: Liver

tag: condition

value: normal

tag: treatment

value: Acetaminophen-Induced Liver Injury (AILI)

tag: time

value: 24 h following AILI

value: Neutrophil

tag: selection marker


title: Neutrophils from PBS livers-7


title: Neutrophils from PBS livers-6


title: siCtrl_RPF

value: Dharmacon (ON-TARGETplus Non-targeting Pool, cat. no. D- 001810-10-05)


title: 12 Gy rep1 cell 90

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H6_mapping.bam

value: Esophageal squamous cell carcinoma line KYSE-180

value: Esophagus


title: siCtrl_RNA


title: 12 Gy rep1 cell 89

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H5_mapping.bam


title: Neutrophils from MC-21 livers-4

value: deficient for Ly6Chi infiltrating monocytes


title: 12 Gy rep1 cell 87

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H3_mapping.bam


title: 12 Gy rep1 cell 88

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H4_mapping.bam


title: Neutrophils from MC-21 livers-3


title: Neutrophils from PBS livers-5


title: Neutrophils from MC-21 livers-2


title: 12 Gy rep1 cell 85

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.H1_mapping.bam


title: 12 Gy rep1 cell 84

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G12_mapping.bam


title: Neurons 4 (Replicate 4)

city: Boston

first: Arpiar

last: Saunders

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: single-cell transcriptome

data_processing:
Sequencing was performed on an Illumina NextSeq500 using a 75 cycle kit (Read1:20bp; Read2: 50 bp)
Sequencing Reads were aligned against the GRCm38.81 mouse genome draft using STAR
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1
A count matrix - called the digital gene expression (DGE) matrix - was output. Columns belong to STAMPs (cells) and transcript counts (rows)
Genome_build: GRCm38.81
Supplementary_files_format_and_content: digital gene expression matrix; comma-delimited file with columns = cells and rows = transcript counts
Supplementary_files_format_and_content: raw_data_genometagged.csv: comma-delimited digital gene expression matrix (ncol = 3102, nrow =16484); each column normalized to 10,000 and log-transformed
Supplementary_files_format_and_content: cluster.barcodes.csv: the barcodes assocated with each of the n=10 clusters following the cluster procedure. See Wallace et al. 2017 Neuron for details. Clustering includes only n=1,118 cells of the total cells found in raw_data_genometagged.csv.

source_name: entopeduncular nucleus (EP) & surrounding regions

extract_protocol: drop-seq (Macosko et al. 2014 Cell)

treatment_protocol: acute brain slices digested for 3 hrs with a protease cocktail before titration, centrifugation to isolate debris-depleted single cells

tag: Sex

value: Male

tag: age


title: 12 Gy rep1 cell 83

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G11_mapping.bam


title: Neurons 3 (Replicate 3)

description: single-cell transcriptome

value: entopeduncular nucleus (EP) & surrounding regions


title: 12 Gy rep1 cell 81

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G9_mapping.bam


title: Neurons 1 (Replicate 1)

description: single-cell transcriptome


title: 12 Gy rep1 cell 82

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G10_mapping.bam


title: Goblet Cells RNA-seq biological rep2

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: processed data file: Read_Counts_All_Cells.txt

data_processing:
Alignment: ATAC-seq and ChIP-seq:bowtie2. RNA-seq: Tophat, version 2.0.6
ATAC-seq peak calling: MACS, version 1.4
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags; read density
Supplementary_files_format_and_content: RNA-Seq: Table with normalized gene expression (RPKM values) for all cell types

source_name: mouse Goblet cells

growth_protocol: Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 0.5U/ml Dispase in DMEM for 30 minutes at 37°C. Cell were stained with antibodies against CD69 (BV421 conjugate, BD Biosciences 562920 ) and CD274 (APC conjugate, BD Biosciences 564715) at 4°C for 30 minutes. CD 69+ 274+ cells were sorted by flow cytometry and immediately used for chromatin transposition.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) followed by DNase treatment with the RNeasy kit (Qiagen).
The SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected with 48 mg/kg DBZ (notch inhibitor) at 0 hours, again at 12 hours, and sacrificed at 115 hours.

tag: strain background

value: B6;129 mixed background

tag: genotype/variation

value: wild type

tag: tissue/cell type

value: Adult Epitheial cells; proximal 1/3 of intestine


title: 12 Gy rep1 cell 80

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G8_mapping.bam

tag: cell line

value: 12 Gy


title: 12 Gy rep1 cell 77

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G5_mapping.bam

tag: tissue


title: 12 Gy rep1 cell 76

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G4_mapping.bam


title: 12 Gy rep1 cell 79

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G7_mapping.bam


title: 12 Gy rep1 cell 78

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G6_mapping.bam


title: 12 Gy rep1 cell 75

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G3_mapping.bam


title: 12 Gy rep1 cell 74

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G2_mapping.bam


title: Control CD274+69+ RNA-seq biological rep2

source_name: CD 274,69 labeled mouse intestinal cells

treatment_protocol: No treatment


title: CD274+69+ DT-Treated RNA-seq biological rep1

source_name: CD 274,69 labeled mouse intestinal cells after DT treatment

treatment_protocol: Mice were injected with diphtheria toxin (50 µg/kg mouse weight) four times on alternate days, and sacrificed 1 day after the last injection.


title: Control CD274+69+ RNA-seq biological rep1

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) followed by DNase treatment with the RNeasy kit (Qiagen).
The TruSeq RNA Sample Preparation Kit V2 (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: 12 Gy rep1 cell 73

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.G1_mapping.bam


title: 12 Gy rep1 cell 72

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F12_mapping.bam


title: 12 Gy rep1 cell 71

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F11_mapping.bam


title: 12 Gy rep1 cell 70

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F10_mapping.bam


description:
Enteroendocrine Cells RNA-seq biological rep2
EntEndo_Rep2

data_processing:
Alignment: ATAC-seq and ChIP-seq:bowtie2. RNA-seq: Tophat, version 2.0.6
ATAC-seq peak calling: MACS, version 1.4
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with normalized gene expression (RPKM values) for all cell types

source_name: mouse Enteroendocrine cells

growth_protocol: Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 0.5U/ml Dispase in DMEM for 30 minutes at 37°C. Cell were stained with antibodies against CD24 (Alexa Fluor 647 conjugate) and Lectin (Lectin from Ulex europaeus - Atto 488 conjugate) at 4°C for 30 minutes. CD 24Hi, UEA-lectin- cells were sorted by flow cytometry and frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.

tag: cell type

value: Wild-Type


title: Paneth Cells RNA-seq biological rep2

description:
Paneth Cells RNA-seq biological rep2
Pan_Rep2

source_name: mouse Paneth cells

growth_protocol: Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 0.5U/ml Dispase in DMEM for 30 minutes at 37°C. Cell were stained with antibodies against CD24 (Alexa Fluor 647 conjugate) and Lectin (Lectin from Ulex europaeus - Atto 488 conjugate) at 4°C for 30 minutes. CD 24Hi, UEA-lectinHi cells were sorted by flow cytometry and frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.


title: Paneth Cells RNA-seq biological rep1

description:
Paneth Cells RNA-seq biological rep1
Pan_Rep1


title: 12 Gy rep1 cell 69

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F9_mapping.bam

tag: irradiation


description:
Enteroendocrine Cells RNA-seq biological rep1
EntEndo_Rep1

tag: genotype


description:
Secretory Progenitors Rbpj RNA-seq biological rep1
SP_Rbpj_Rep1

source_name: mouse secretory progenitor cells

growth_protocol: Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.

treatment_protocol: Mice were injected with twice daily dose of 2mg Tamoxifen for 2 consecutive days, to activate tamoxifen-inducible Cre and recombine conditional alleles, and sacrificed on day 3.

value: Rbpj F/F; Villin-CRE


description:
Secretory Progenitors Rbpj RNA-seq biological rep2
SP_Rbpj_Rep2


title: Goblet Cells RNA-seq biological rep1

description: processed data file: Read_Counts_All_Cells.txt


title: 12 Gy rep1 cell 68

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F8_mapping.bam


description:
Secretory Progenitors DBZ RNA-seq biological rep2
SP_DBZ_Rep2

treatment_protocol: Mice were injected with 48 mg/kg DBZ (notch inhibitor) at 0 hours, again at 12 hours, and sacrificed at 38 hours.

value: Atoh1 F/F


title: 12 Gy rep1 cell 67

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F7_mapping.bam


title: 12 Gy rep1 cell 65

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F5_mapping.bam


title: 12 Gy rep1 cell 66

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F6_mapping.bam


description:
Secretory Progenitors DBZ RNA-seq biological rep1
SP_DBZ_Rep1


title: Enterocyte Progenitor H3K4me1 ChIP-seq biological rep2

source_name: mouse enterocyte progenitor cells

growth_protocol: Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.

extract_protocol:
Whole cell lysates were sonicated and incubated with 2 ug H3K4me1 antibody overnight (C15410194, Diagenode) for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Atoh1 F/F; Villin-CRE


description:
Bmi1-GFP-Irradiated RNA-seq 36hr biological rep1
Bmi1_10GyRad_36hr

source_name: Bmi1-GFP+ mouse intestinal cells after irradiation

growth_protocol: Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Bmi1-GFP+ve cells were sorted by flow cytometry. Cells were frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.

treatment_protocol: Mice were given whole body radiation dose of 10Gy  and intestinal tissue was harvested after 36 hours.


description:
Enterocyte Prgenitors RNA-seq biological rep1
EP_Rep1

treatment_protocol: Mice were injected with 1mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles, and sacrificed after 3 weeks.


title: 12 Gy rep1 cell 62

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F2_mapping.bam


title: 12 Gy rep1 cell 63

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F3_mapping.bam


title: 12 Gy rep1 cell 61

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.F1_mapping.bam


description:
Enterocyte Progenitor RNA-seq biological rep2
EP_Rep2


description:
Lgr5-GFP-DTR ISC RNA-seq biological rep1
Lgr5_GFP-DTR_Rep1

source_name: Lgr5-GFP-DTR+ mouse intestinal stem cells

growth_protocol: Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Lgr5-GFP+ve intestinal stem cells were sorted by flow cytometry. Cells were frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.


title: 12 Gy rep1 cell 59

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E11_mapping.bam


description:
Lgr5-GFP-Cre ISC RNA-seq biological rep3
Lgr5_GFP-Cre_Rep3

source_name: Lgr5-GFP-Cre+ mouse intestinal stem cells

growth_protocol: Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Lgr5-GFP-HI intestinal stem cells were sorted by flow cytometry. Cells were frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.


title: 12 Gy rep1 cell 60

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E12_mapping.bam


description:
Lgr5-GFP-Cre ISC RNA-seq biological rep2
Lgr5_GFP-Cre_Rep2


title: 12 Gy rep1 cell 58

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E10_mapping.bam


title: 12 Gy rep1 cell 57

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E9_mapping.bam


title: 12 Gy rep1 cell 56

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E8_mapping.bam


description:
Lgr5-GFP-Cre ISC RNA-seq biological rep1
Lgr5_GFP-Cre_Rep1


description:
Control Bmi1-GFP RNA-seq biological rep3
Bmi1_Rep3

source_name: Bmi1-GFP+ mouse intestinal cells


description:
Control Bmi1-GFP RNA-seq biological rep2
Bmi1_Rep2


title: 12 Gy rep1 cell 55

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E7_mapping.bam


title: 12 Gy rep1 cell 53

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E5_mapping.bam


description:
Lgr5-GFP-DTR ISC RNA-seq biological rep2
Lgr5_GFP-DTR_Rep2


title: 12 Gy rep1 cell 54

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E6_mapping.bam


title: 12 Gy rep1 cell 52

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E4_mapping.bam


title: Secretory Progenitors H3K27Ac ChIP-seq biological rep1

extract_protocol:
Whole cell lysates were sonicated and incubated with 5 ug H3K27Ac antibody overnight (39135, Active MOtif) for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Secretory Progenitors H3K4me1 ChIP-seq biological rep1


title: Secretory Progenitors H3K4me1 ChIP-seq biological rep2


title: Secretory Progenitors H3K4me2 ChIP-seq biological rep1

extract_protocol:
Whole cell lysates were sonicated and incubated with 5 ul H3K4me2 antibody overnight (07-030, Millipore) for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


description:
Control Bmi1-GFP RNA-seq biological rep1
Bmi1_Rep1


title: Enterocyte Progenitor H3K27Ac ChIP-seq biological rep1


title: 12 Gy rep1 cell 51

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E3_mapping.bam


title: 12 Gy rep1 cell 50

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E2_mapping.bam


title: 12 Gy rep1 cell 49

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.E1_mapping.bam


title: CD274+69+ DT-Treated RNA-seq biological rep2

description: processed data file: Read_Counts_All_Cells.txt


title: Enterocyte Progenitors H3K4me2 ChIP-seq biological rep1

description: Enterocyte Prgenitors H3K4me2 ChIP-seq biological rep1


title: 12 Gy rep1 cell 47

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D11_mapping.bam


title: 12 Gy rep1 cell 45

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D9_mapping.bam


title: 12 Gy rep1 cell 44

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D8_mapping.bam


title: Control CD274+69+ ATAC Biological rep2

description:
Control CD274+69+ ATAC Biological rep2
CD274+69+_ATAC.bw

data_processing:
Library strategy: ATAC-seq
Alignment: ATAC-seq and ChIP-seq:bowtie2. RNA-seq: Tophat, version 2.0.6
ATAC-seq peak calling: MACS, version 1.4
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with normalized gene expression (RPKM values) for all cell types

extract_protocol:
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


description:
CD274+69+ DT-Treated ATAC Biological rep1
CD274+69+_DT-Treated_ATAC.bw


title: Control CD274+69+ ATAC Biological rep1

description:
Control CD274+69+ ATAC Biological rep1
CD274+69+_ATAC.bw


title: 12 Gy rep1 cell 43

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D7_mapping.bam


description:
Bmi1-GFP-Irradiated ATAC 36hr biological rep2
Bmi1_Rad_36hr_ATAC.bw

growth_protocol: Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Bmi1-GFP+ve cells were sorted by flow cytometry. Cell were immediately used for chromatin transposition.


title: 12 Gy rep1 cell 41

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D5_mapping.bam


title: 12 Gy rep1 cell 42

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D6_mapping.bam


title: 12 Gy rep1 cell 48

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D12_mapping.bam


title: 12 Gy rep1 cell 39

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D3_mapping.bam


description:
Secretory Progenitors ATAC biological rep1
SP_ATAC.bw

growth_protocol: Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C. Cell were immediately used for chromatin transposition.


description:
Secretory Progenitors ATAC biological rep2
SP_ATAC.bw


title: Enterocyte Progenitor H3K4me1 ChIP-seq biological rep1


description:
Enterocyte Progenitor ATAC biological rep2
EP_ATAC.bw


description:
Bmi1-GFP-Irradiated ATAC 24hr biological rep1
Bmi1_Rad_24hr_ATAC.bw

treatment_protocol: Mice were given whole body radiation dose of 10Gy  and intestinal tissue was harvested after 24 hours.


title: 12 Gy rep1 cell 38

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D2_mapping.bam


description:
CD274+69+ DT-Treated ATAC Biological rep2
CD274+69+_DT-Treated_ATAC.bw


title: 12 Gy rep1 cell 35

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C11_mapping.bam


title: Lgr5-GFP ISC ATAC biological rep2

description:
Lgr5-GFP ISC ATAC biological rep2
Lgr5_ATAC.bw

growth_protocol: Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Lgr5-GFP-HI intestinal stem cells were sorted by flow cytometry. Cell were immediately used for chromatin transposition.


title: 12 Gy rep1 cell 40

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D4_mapping.bam


title: 12 Gy rep1 cell 33

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C9_mapping.bam


title: 12 Gy rep1 cell 46

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D10_mapping.bam


title: 12 Gy rep1 cell 36

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C12_mapping.bam


title: 12 Gy rep1 cell 37

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.D1_mapping.bam


title: 12 Gy rep1 cell 32

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C8_mapping.bam


title: Control Bmi1-GFP ATAC biological rep2

description:
Control Bmi1-GFP ATAC biological rep2
Bmi1_ATAC.bw


title: 12 Gy rep1 cell 31

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C7_mapping.bam


title: Control Bmi1-GFP ATAC biological rep1

description:
Control Bmi1-GFP ATAC biological rep1
Bmi1_ATAC.bw


title: 12 Gy rep1 cell 30

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C6_mapping.bam


title: Lgr5-GFP ISC ATAC biological rep1

description:
Lgr5-GFP ISC ATAC biological rep1
Lgr5_ATAC.bw


description:
Bmi1-GFP-Irradiated ATAC 36hr biological rep1
Bmi1_Rad_36hr_ATAC.bw


description:
Bmi1-GFP-Irradiated ATAC 24hr biological rep2
Bmi1_Rad_24hr_ATAC.bw


title: MDA97

city: Houston

first: Andrea

last: Ochoa

state: TX

address: 1515 Holcombe

institute: UT MD Anderson Cancer Center

data_processing: The TorrentSuite Software was used to extract all fastq files, and total counts data.

source_name: Bladder tumor

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit. Quality control was performed by NanoDrop ND-1000 and Agilent Bioanalyzer. 20 ng of small RNA was used for cDNA library preparation using the Ion Total RNA-Seq Kit v2. The Agilent Bioanalyzer was used to quantitate the cDNA library.
Ion Total RNA-Seq Kit v2

value: bladder tumor

tag: cstage

tag: age (at specimen collection)

tag: os censor

value: censored

tag: dss censor

tag: survival (mo)


title: 12 Gy rep1 cell 28

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C4_mapping.bam

source_name: Esophageal squamous cell carcinoma


title: 12 Gy rep1 cell 27

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C3_mapping.bam


description:
Enterocyte Progenitors ATAC biological rep1
EP_ATAC.bw

tag: strain


title: 12 Gy rep1 cell 25

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C1_mapping.bam


title: 12 Gy rep1 cell 24

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B12_mapping.bam


title: 12 Gy rep1 cell 26

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C2_mapping.bam


title: 12 Gy rep1 cell 23

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B11_mapping.bam


title: 12 Gy rep1 cell 21

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B9_mapping.bam


title: MDA85

value: uncensored


title: MDA77


title: 12 Gy rep1 cell 22

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B10_mapping.bam


title: MDA89


title: 12 Gy rep1 cell 20

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B8_mapping.bam


title: MDA94


title: MDA91


title: MDA73


title: MDA74


title: 12 Gy rep1 cell 18

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B6_mapping.bam


title: 12 Gy rep1 cell 19

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B7_mapping.bam


title: MDA72


title: MDA71


title: 12 Gy rep1 cell 29

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.C5_mapping.bam


title: MDA69


title: MDA99


title: MDA95


title: MDA70


title: 12 Gy rep1 cell 15

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B3_mapping.bam


title: 12 Gy rep1 cell 16

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B4_mapping.bam


title: MDA68


title: 12 Gy rep1 cell 14

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B2_mapping.bam


title: MDA63


title: 12 Gy rep1 cell 13

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B1_mapping.bam


title: NH008

first: Yanhui

last: Hu

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Drosophila  genome (Drosphila genome BDGP6) with STAR version 2.5.3 and the alignments were evaluated based on the mappability to transcripts and the complexity of the transcriptome as well as the quality among other custom metrics.
The expression of transcripts was quantified using Sailfish 0.10.1 taking 30 bootstrap samples for each sample.  Gene level expressions were calculated by collapsing the transcript-level quantification with tximport.
Genome_build: Drosphila genome BDGP6
Supplementary_files_format_and_content: text files with TPM values of all samples for each gene or transcript

organism: Drosophila melanogaster

source_name: larval fat body

growth_protocol: Flies were raised at 25°C following standard procedures unless otherwise noted

extract_protocol:
RNA was harvested using Trizol reagent.
After assessing RNA quality with an Agilent Bioanalyzer, libraries constructed with an Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold.

treatment_protocol: Fed or starvation for 4 hours or 16 hours

tag: starvation status

value: 16 hour starvation

value: fat body

tag: developmental stage

value: larval


title: MDA61


title: NH007


title: 12 Gy rep1 cell 17

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.B5_mapping.bam

value: Esophageal squamous cell carcinoma line KYSE-180

value: Esophagus


title: NH004

value: OreR (wild-type)

value: 4 hour starvation


title: NH003


title: MDA60


title: 12 Gy rep1 cell 10

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A10_mapping.bam


title: 12 Gy rep1 cell 9

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A9_mapping.bam


title: 12 Gy rep1 cell 12

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A12_mapping.bam


title: NH001

value: fed


title: NH005


title: NH006


title: 12 Gy rep1 cell 8

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A8_mapping.bam


title: 12 Gy rep1 cell 11

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A11_mapping.bam


title: 12 Gy rep1 cell 7

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A7_mapping.bam


title: NH002


title: MDA55


title: MDA66


title: MDA54


title: MDA58


title: 12 Gy rep1 cell 6

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A6_mapping.bam


title: MDA53


title: MDA59


title: 12 Gy rep1 cell 5

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A5_mapping.bam


title: MDA51


title: MDA50


title: 12 Gy rep1 cell 4

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A4_mapping.bam


title: 12 Gy rep1 cell 3

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A3_mapping.bam


title: 12 Gy rep1 cell 2

description: Corresponds to Normalized_counts.txt column: merge_Sample_Pan_C.A2_mapping.bam


title: MDA49


title: MDA46


title: MDA47


title: MDA57


title: 0 Gy cell 42

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T48.bam

value: 0 Gy


title: E3M0c

city: New Haven

first: Yajaira

last: Suarez

state: Connecticut

address: 10 Amistad Street

department: Comparative Medicine

institute: Yale University School of Medicine

description: Biological Replicate 2

data_processing:
MicroRNA sequencing results were trimmed and mapped to miRBase mouse stem-loop sequences (http://www.mirbase.org/) using the mirDeep2 software.
The alignment reads were normalized as proportion of total reads mapped to any know miRNAs in each sample.
differential expression analysis using DESeq2.
Genome_build: miRBase mouse stem-loop sequences (http://www.mirbase.org/)
Supplementary_files_format_and_content: tab-delimited text files include RPM. Readss mapped to a miRNA Per million total mapped reads

source_name: unstimulated BMDMs

extract_protocol:
Total RNA from unstimulated BMDMs was extracted using and miRNA isolation Kit (Qiagen) followed by DNAse treatment to remove genomic contamination using RNA MinElute Cleanup (Qiagen). The purity and integrity of total RNA sample was verified using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina).
Small RNA libraries from WT BMDMs were performed TrueSeq Small RNA Library preparation (Illumina) and were sequenced on Illumina HiSeq 2000 platform (2 x 50bp read length).

value: wild type

tag: age

value: 8 weeks

value: Bone Marrow derived macrophages (BMDMs)


title: 0 Gy cell 40

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T46.bam


title: 0 Gy cell 39

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T45.bam


title: MDA43


title: MDA45


title: MDA31


title: 0 Gy cell 37

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T42.bam


title: MDA42


title: 0 Gy cell 36

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T41.bam


title: 0 Gy cell 35

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T40.bam


title: MA9_CreER_48hrs_1

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

description: RNA was extracted from established cell lines

data_processing:
Raw reads were decoded and converted to Fastq files.
Fastq files were aligned to genome mm10 using Tophat2.1 and Bowtie2 using default parameters.
Transcripts were assembled, assigned to genes, and were quantified using the tool suite Cufflinks 2.1 (including Cufflinks, Cuffmerge, and Cuffdiff).
Genome_build: mm10
Supplementary_files_format_and_content: processed data is presented as it was outputed from Cuffdiff in a .txt document providing FPKM values for all samples and controls as well as q-values and fold-change values.

molecule: polyA RNA

source_name: Mouse AML derived from mouse bone marrow

growth_protocol: Cells were grown in IMDM + 15% stem cell qualified FBS + 1%pen/strep + 10ng/mL IL-3

extract_protocol:
RNA was extracted using the Qiagen Rneasy kit
Adapters were ligated and the libraries were sequenced using the Illumina HiSeq Libraries platform

treatment_protocol: Cells were treated with 7.5nM 4-hydroxytamoxifen (4OHT) for 24 or 48 hours.

value: Cdc73 +/+ CreERT2

tag: treatment

tag: time


title: MA9_CreER_48hrs_2


title: MDA24


title: MA9_Cdc73flCreER_48hrs_2

value: Cdc73fl/fl CreERT2


title: MA9_Cdc73flCreER_48hrs_1


title: MA9_CreER_24hrs_2


title: MDA149

value: bladder tumor


title: 0 Gy cell 33

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T37.bam


title: MA9_CreER_24hrs_1


title: 0 Gy cell 34

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T39.bam


title: MA9_Cdc73flCreER_24hrs_2


title: MDA145

value: censored


title: 0 Gy cell 41

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T47.bam


title: E2M0c

description: Biological Replicate 1

tag: strain background

tag: genotype/variation


title: 0 Gy cell 32

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T36.bam

tag: cell line

tag: tissue


title: MA9_Cdc73flCreER_24hrs_1


title: 0 Gy cell 31

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T35.bam

tag: irradiation


title: 0 Gy cell 30

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T34.bam


title: Jak2_Hmga2

city: Fukushima

first: Kazuhiko

last: Ikeda

state: Fukushima

address: 1 Hikariga-oka

department: Blood Transfusion and Transplantation Immunology

country: Japan

institute: Fukushima Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per kilobase of exon per million reads mapped (FPKM) were calculated using standard formula.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: LSK cells

extract_protocol:
LSK cells were sorted from bone marrow cells and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols

tag: cell type

value: HSC-enriched LSK cells

value: JAK2V617F/Hmga2 double-Tg


title: MDA141

tag: cstage


title: 0 Gy cell 29

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T33.bam


title: MDA140

tag: age (at specimen collection)

value: uncensored


title: MDA20

tag: os censor


title: MDA137

tag: dss censor


title: 0 Gy cell 28

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T31.bam


title: MDA136

tag: survival (mo)


title: Jak2_Ezh2

tag: strain

value: JAK2V617F-Tg/EZH2 conditional KO


title: 0 Gy cell 27

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T30.bam

value: Esophageal squamous cell carcinoma line KYSE-180


title: Jak2


title: Hmga2


title: WT

description: WT

value: WT


title: 0 Gy cell 26

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T29.bam

value: Esophagus


title: MDA133


title: MDA132


title: CS_9months_rep5

city: Denver

first: Irina

last: Petrache

state: CO

address: 1400 Jackson St, Molly Blank Building, J203

department: Division of Pulmonary, Critical Care and Sleep Medicine

institute: National Jewish Health

description:
RNA from mouse x129 (treatment CS after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv

data_processing:
Sequences were mapped to the Mus musculus reference genome (mm10) using GSNAP version 2013-11-27 with SNP version 137
Uniquely mapped reads were quantified with HTSeq (version 0.5.4p3) using the “intersection-nonempty” mode; counts from the four sequencing lanes for each sample were added up.
Low expression genes were filtered across the entire time series using HTSFilter (version 1.8.0) and DESeq normalization applied from with HTSFilter. Month 9 cessation data was filtered separately for additional analysis
For DEXseq analysis, uniquely mapped reads were quantified using exon part derived from Ensembl annotation (version 78 for mouse) with HTSeq (version 0.6.0) and the dexseq_count.py script supplied by the DEXSeq package.  Counts from the four sequencing lanes for each sample were added up.
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values file containing raw read counts; first column contains gene names, first row contains mouse IDs (see Samples for details)
Supplementary_files_format_and_content: DEXSeq-counts.txt: raw counts for exonic parts
Supplementary_files_format_and_content: mouse126_all_reads.csv: CSV; raw read counts, all genes
Supplementary_files_format_and_content: mouse126_filtered_reads.csv: CSV; raw read counts, filtered genes
Supplementary_files_format_and_content: mouse126_filtered_9month_reads.csv: CSV; raw read counts, filtered separately for 9 month cessation data

source_name: Whole lung

extract_protocol:
Whole lung tissue was snap-frozen and stored at -80 °C.   RNA was extracted using RNeasy Mini Kits (Qiagen, # 74104) following standard protocols.
Total RNA (500ng per sample) was used to construct sequencing libraries with the Illumina TruSeq Stranded mRNA LT Library Construction Kit (catalog # RS-122-2101, Illumina Inc., San Diego, CA) following standard protocols.  Each library was sequenced on 4 lanes spread over two different flow cells on an Illumina HiSeq 2000 sequencer.

tag: mouse id

value: whole lung

tag: time point

value: 9 months

value: CS


title: 0 Gy cell 25

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T28.bam

value: 0 Gy


title: MDA130


title: MDA129


title: CS_9months_rep4

description:
RNA from mouse x128 (treatment CS after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv


title: 0 Gy cell 24

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T27.bam


title: 0 Gy cell 23

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T26.bam


title: MDA143


title: CS_9months_rep2

description:
RNA from mouse x126 (treatment CS after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv


title: MDA128


title: MDA124


title: CS_6months_rep5

description:
RNA from mouse x99 (treatment CS after 6 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 6 months


title: 0 Gy cell 20

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T23.bam


title: 0 Gy cell 19

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T21.bam


title: CS_6months_rep4

description:
RNA from mouse x98 (treatment CS after 6 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: MDA120


title: MDA119


title: MDA118


title: 0 Gy cell 17

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T19.bam


title: 0 Gy cell 16

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T18.bam


title: MDA116


title: 0 Gy cell 18

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T20.bam


title: CS_6months_rep1

description:
RNA from mouse x100 (treatment CS after 6 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: CS_9months_rep3

description:
RNA from mouse x127 (treatment CS after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv


title: MDA114


title: 0 Gy cell 15

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T17.bam


title: MDA112


title: 0 Gy cell 22

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T25.bam


title: CS_3months_rep4

description:
RNA from mouse x79 (treatment CS after 3 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 3 months


title: CS_9months_rep1

description:
RNA from mouse x107 (treatment CS after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv


title: 0 Gy cell 21

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T24.bam


title: CS_3months_rep5

description:
RNA from mouse x80 (treatment CS after 3 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: 0 Gy cell 14

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T15.bam


title: MDA111


title: CS_3months_rep3

description:
RNA from mouse x78 (treatment CS after 3 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: 0 Gy cell 13

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T14.bam


title: MDA110


title: CS_6months_rep3

description:
RNA from mouse x89 (treatment CS after 6 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: CS_3months_rep2

description:
RNA from mouse x68 (treatment CS after 3 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: 0 Gy cell 12

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T13.bam


title: R_NSCP1_lncRNA

city: shenzhen

first: Guanyu

last: Ji

state: GuangDong

address: 14th of middle jinxiu road

department: R&D

institute: GENEDOHEALTH

description:
lncRNA
lncRNA.fpkm.txt

data_processing:
MeDIP-seq: Illumina Casava1.7 software used for basecalling.
MeDIP-seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rheMac3 whole genome using bwa-0.7.7 with default parameters.
MeDIP-seq: enrich information of peaks was analysised using MACS2
Genome_build: MeDIP-seq: rhesus monkey(rheMac3,which is based on the genome of a five-year-old female Macaca mulatta originating from the South-West of China,Genome infomation can be downloaded from http://genome.ucsc.edu/cgi-bin/hgGateway?db=rheMac3)
Supplementary_files_format_and_content: MeDIP-seq: tab-delimited text files include peaks information of rhesus monkey.
lncRNA-Seq: Illumina Casava1.7 software used for basecalling.
lncRNA-Seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rheMac3 whole genome using tophat v2.0.11 with parameters -r 200 -p 4 -N 7 --read-gap-langth 10
lncRNA-Seq: Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: lncRNA-Seq: rhesus monkey(rheMac3,which is based on the genome of a five-year-old female Macaca mulatta originating from the South-West of China,Genome infomation can be downloaded from http://genome.ucsc.edu/cgi-bin/hgGateway?db=rheMac3)
Supplementary_files_format_and_content: lncRNA-Seq: tab-delimited text files include FPKM value information of rhesus monkey.

organism: Macaca mulatta

source_name: rhesus monkey

extract_protocol:
For lncRNA deep sequencing, total RNAs of ESCs and R-NSCP1 were isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions. The the ribosomal RNAs were removed by using rRNA Removal Kit (Epicentre, Madison, WI, USA). Subsequently, the rRNA-depleted RNAs were processed using the NEBNext Ultra Directional RNA Library Prep Kit from Illumina (NEB, Ipswich, MA, USA), following manufacturer’s recommendations. The quality of libraries was assessed by the Agilent Bioanalyzer 2100 system.
lncRNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cell


title: CS_3months_rep1

description:
RNA from mouse x66 (treatment CS after 3 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: CS_6months_rep2

description:
RNA from mouse x88 (treatment CS after 6 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: rESC_lncRNA

description:
lncRNA
lncRNA.fpkm.txt


title: 0 Gy cell 11

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T12.bam

extract_protocol:
Cells were directly lysed and amplified with smart-seq2 kit
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Input_MeDIP-seq

description: total DNA

extract_protocol:
For MeDIP-seq, Genomic DNA (gDNA) was extracted from cells using a DNeasy Blood and Tissue kit (Qiagen, Chatsworth, CA, USA) according to the manufacturer's instructions. DNA sonication , Illumina's paired-end library preparation and methylated DNA immunoprecipitation were performed   as previously described (Feber et al., 2011). Briefly, five micrograms of gDNA were randomly sheared to a median fragment size of 200 bp using a Covaris S220. Sonicated DNAs were subjected to library preparation according to Illumina Paired End libraries preparation protocols. Then methylated DNA immunoprecipitation was performed using the Methylated-DNA IP kit (Zymo Research; Orange, CA, USA)
MeDIP libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cell (mixed input of  rESC and RNSCP1)


title: MDA109

value: bladder tumor


title: MDA108

value: censored


title: R_NSCP1.MeDIP-seq

description: total DNA


title: CS_1month_rep4

description:
RNA from mouse x56 (treatment CS after 1 month)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 1 month


title: MDA104


title: 0 Gy cell 9

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T09.bam


title: 0 Gy cell 8

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T08.bam


title: CS_1month_rep3

description:
RNA from mouse x50 (treatment CS after 1 month)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: MDA103


title: rESC_MeDIP-seq

description: total DNA


title: col0.old3.r2

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

data_processing:
FastaQ files of each sample was aligned against Arabidopsis Genome TAIR 10 using TopHat.
Mapped sequences were assembled into transcripts using Cufflinks.
Assembled transcripts of each sample were summarized and merged into transcription units using Cuffcompare.
Expression level of each TU are presented by Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: Arabidopsis Genome Annotation TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample produced by Cufflinks,Cuffcompare and Cuffdiff.

organism: Arabidopsis thaliana

source_name: Another Col-0

growth_protocol: Arabidopsis plant  materials were grown under long day conditions at 22℃. Seedling were collected from 2-week old plants that grew in soil.

extract_protocol:
All samples were harvested and frozen immediately in liquid nitrogen until use. Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen). RNA sequence libraries were prepared with TruSeq RNA sample Prep V2 kit according to the instructions (Illumina). Sequences were determined by HiSeq 2500 sequencing system in the genomic center in Rockefeller University.
101-nt Single-end RNA-seq by Illumina HiSeq 2500

value: 2-week seedlings

tag: ecotype

tag: replicate

value: Biological repliate 2


title: col0.old3.r1

value: Biological repliate 1


title: CS_1month_rep2

description:
RNA from mouse x49 (treatment CS after 1 month)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

tag: treatment


title: Pineal Night rep3

city: New York

first: Marjan

last: Bozinoski

address: 1305 York Avenue, Box 140

department: Physiology and Biophysics

institute: Weill Cornell Medicine

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads were aligned with the RNA-STAR aligner (v. 2.3.0e) , using a rhesus rheMac3 genome build. STAR aligner parameters used: --runThreadN 8 --outFilterMultimapNmax 1 --outSAMunmapped Within --outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in-house written scripts, and no major artifacts or abnormalities were found
Gene read counts were provided by R subreads package, (featureCounts function) with parameters specifying: paired-end reads, and reverse-complement for the second strand (-p, -S2). Annotation for assigning the reads was derived from Gencode v.19 human annotation. Gene coordinates were lifted over using RheMac3/hg19 liftover chains, and only sequences that shared no less than 95% homology were kept, resulting in total of 50308 genes. Differential expression analysis was performed using DESeq2 software package.
Genome_build: RheMac3
Supplementary_files_format_and_content: retina_pineal_control.xlsx file includes FPKM values for all of the Samples, pineal_DE.xlsx includes the differential expression analysis for pineal gland, Retina_DE.xlsx includes the differential expression analysis for retiina

source_name: Pineal Night

extract_protocol:
Twelve adult rhesus macaques (Macaca mulatta, 3 to 33 years of age, male and female, 4 to 10.3 kg) were obtained through the Veterinary Resources Program Primate Recycle Program of NIH over a period of 11 years.     All protocols and handling of the animals conformed to the Guidelines for Care and Use of Laboratory Animals (NIH Publication 80-23; Protocols 99-012 and 11-055 ). Animals were housed under a 12-h light, 12-h dark lighting regimen (lights on at 0600 h) in NIH facilities for at least 6 wk. The light level in the cages was approximately 325 Lux.   Animals (three per time point) were sacrificed between 1100 and 1300 (day) , 1700 and 1900 (dusk), 2300 and 0100 (night) and 0500 and 0700 (dawn).  Animals were anesthetized (ketamine, 0.1 ml/kg body weight) and a catheter was placed in the saphenous vein prior to transport to the procedure room.   Animals were sacrificed using Euthasol (Virbac, Fort Worth, TX)  or Beuthanasia D ( Schering Plough, Union, NJ).   Animals sampled at night  or dusk  were anesthesized  under dim red light and  blindfolded; euthanasia was done under dim white light and  the blindfold was removed  after decapitation. Removal of tissues, including the pineal gland, retina, and others (corpus callosum, frontal cortex, cerebellum, thalamus, hippocampus, caudate, medulla, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine,  testis and  ovary) was complete within 45 minutes following euthanasia; immediately following removal, samples  of each tissue were obtained and placed on solid  CO2.  Tissue was store at -80° C. Total RNA was extracted from individual pineal glands or pieces of other tissues (  2 to 4 mm 3 pieces) with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: Night

value: pineal gland


title: 0 Gy cell 7

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T07.bam

value: Esophageal squamous cell carcinoma line KYSE-180

value: Esophagus


title: Pineal Night rep1


title: Pineal Night rep2


title: CS_1month_rep1

description:
RNA from mouse x47 (treatment CS after 1 month)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: whole lung


title: 0 Gy cell 6

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T06.bam


title: col0.tair1.r2

source_name: SALK Col-0

value: SALK Col-0

tag: genotype/variation

value: WT


title: 0 Gy cell 5

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T05.bam

tag: cell line

value: 0 Gy


title: CS_7days_rep4

description:
RNA from mouse x29 (treatment CS after 7 days)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

tag: tissue

value: 7 days

value: CS


title: Pineal Dusk rep3

source_name: Pineal Dusk

value: Dusk


title: CS_1month_rep5

description:
RNA from mouse x59 (treatment CS after 1 month)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: col0.tair1.r1


title: 0 Gy cell 10

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T11.bam

tag: irradiation


title: 0 Gy cell 4

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T04.bam


title: Pineal Dusk rep2


title: 0 Gy cell 3

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T03.bam


title: Pineal Dusk rep1


title: CS_7days_rep3

description:
RNA from mouse x28 (treatment CS after 7 days)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: CS_7days_rep2

description:
RNA from mouse x27 (treatment CS after 7 days)
mouse126_all_reads.csv
mouse126_filtered_reads.csv