title: SAM24294907 Intestine Small S4_EpCAM_48h bulk AKVPL 48h Saline

description:
timepoint: 48h
treatment_name: Saline


title: SAM24294904 Intestine Small S1_EpCAM_48h bulk AKVPL 48h Saline

status: Public on Mar 29 2017

type: SRA

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

country: USA

institute: Genentech Inc.

description:
timepoint: 48h
treatment_name: Saline

library_source: transcriptomic

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

molecule: polyA RNA

organism: Mus musculus

source_name: small intestine

extract_protocol: After FACS, cells were centrifuged at 1200rpm for 5 minutes. RNA was extracted from samples using the RNeasy Micro kit (cat # 74004; Qiagen) according to the manufacturer’s instructions and resuspended in a volume of 14ul. RNA quality was evaluated using Bioanalyzer.

value: Intestine Small

tag: sort

value: bulk

tag: genotype

value: AKVPL


title: C_60m_cR03_p08_62_TAATGCGC-TAATCTTA_L00M_R1_001

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Base calls were performed using CASAVA v. 1.8.2
Reads were aligned to Amel_4.5 (OGS v. 3.2 annotation set) using TopHat2 v. 2.0.10 with Bowtie2 v. 2.1.0 and Samtools v. 0.1.19
Deformed Wing Virus (DWV) alignments were calculated by aligning to the Pennsylvania variant of the DWV genome (GenBank accession: AY292384) using Bowtie 2 v. 2.1.0, and filtering took place during downstream bioinformatic analysis
Tags were counted using htseq-count in HTSeq v. 0.6.1
Genome_build: Amel_4.5 (OGS v. 3.2 annotation) with Pennsylvania build of DWV (GenBank accession: AY292384)
Supplementary_files_format_and_content: tab-delimited tag counts were generated using htseq-count.

molecule: total RNA

organism: Apis mellifera

source_name: mushroom body

growth_protocol: Honey bee (Apis mellifera) workers were obtained from colonies maintained in apiaries according to standard commercial methods by the University of Illinois Bee Research Facility, Urbana, IL, from June to August 2013 and 2014. For the RNA-Seq experiment, we used three colonies, each headed by a queen that was instrumentally inseminated with semen from a single (different) drone (Single Drone Inseminated colony, “SDI”); because of hapolodiploidy, the resulting female worker offspring were highly related to each other (average coefficient of relatedness, r = 0.75), thus decreasing within-trial genetic variation. One-day-old adult bees were obtained by removing frames of honeycomb containing pupae from colonies, placing them in an incubator (34°C, 50% relative humidity), and then monitoring their emergence every 24 h.

extract_protocol:
Bee heads were separated from bodies on dry ice and placed in a dissection dish with pure ethanol and dry ice to prevent RNA degradation during dissection. The cuticle of the head capsule was removed and each head was placed in RNAlaterICE (Life Technologies) at -20ºC for 14 to 18 h. The heads were then opened, the hypopharyngeal glands removed, and the whole brain removed. Using a fine scalpel, the optic lobes were removed and a horizontal incision was made across the midbrain through the posterior protocerebral lobe. The lower part of the midbrain containing the antennal lobes and the subesophageal ganglion were removed. The upper part of the midbrain containing mostly the mushroom bodies (MB) and the central brain was used for gene expression analysis. The MBs were placed in a new 1.5ml tube and kept frozen (-80°C) until RNA extraction. RNA extraction was performed with a PicoPure RNA Isolation Kit (Applied Biosystems; Lot #: 1210063) and the standard protocol, including DNase treatment (QIAGEN) to remove genomic DNA contamination. 500 ng RNA from each sample (except for 5 samples that yielded 350- 500 ng) were used for whole mRNA expression analysis.
RNA-Seq libraries were constructed with the TruSeq® Stranded mRNA HT (high throughput kit, Illumina cat #: RS-122-2103) using an ePMotion 5075 robot (Eppendorf) The libraries were pooled in equimolar concentration as per instructions and each pool was quantitated by qPCR. Single-end sequencing (read length = 100nt) was performed on an Illumina HiSeq2000 using a TruSeq SBS sequencing kit version 3.

treatment_protocol: Groups were created by dividing emerged bees into groups of ten, individually marking on their thoraces with a spot of paint (Testor’s PLA), and keeping them in clear plastic Petri dishes (100 x 20 mm). The dishes were supplied with one 2 ml tube of 30% sucrose solution and one small piece of honeycomb containing honey (containing about 6 cells). Groups were held in the incubator for 7 days prior to the beginning of the experiment. Behavioral assays were performed in an observation room under conditions (28°C, 30% relative humidity) that are within the normal range that occurs in our locality at the hive entrance, where colony defense normally occurs. The dishes of bees were placed in the observation room for at least 30 min prior the beginning of the behavioral assay for acclimatization. To start the behavioral assay, an unrelated intruder bee was introduced to each group for 5 min, during which the response of each bee toward the intruder was recorded. Detailed scan sampling observations of each bee were made every 10 s for the entire 5-min introduction period, according to a well-established scoring system. Five different behaviors were recorded and scored based on their relative aggression intensity ranking as follows: 1- Antennation and/or Trophallaxis; 2- Opening of the mandibles; 3- Chasing and/or Lunging; 4- Biting the Intruder; and 5- Attempting to Sting or Stinging. Inter-observer assays were conducted to ensure that all observers involve in this study scored the behaviors similarly. Bees were assigned randomly to experimental or control treatments. For groups assigned to the experimental treatment, the intruder assay was performed as described above. For groups assigned to the control treatment, a small tube (200µl) similar in size to a worker bee was introduced to the group; although bees occasionally inspected the object, its presence did not elicit aggression or alter their behavior in any discernable way. To prevent odors from accumulating, each tube was used only once. The intruder bee and the control tube were introduced simultaneously (each to its respective group) and removed at the end of the 5-min assay. The resident bees were then left undisturbed for 30, 60 or 120 min. The most aggressive bee in each experimental group (responding with at least biting and/or stinging attempts for more than 30 sec) was selected for transcriptomic analysis, and a randomly selected bee from the control group was collected at the same time for comparison. These bees were frozen immediately in liquid nitrogen and individually placed in a 1.5ml tube stored in a -80°C freezer for further analysis. For transcriptomic profiling, 10 pairs of experimental bees and matched control bees were used for each time point, summing to a total of 60 bees per colony. The experiment was repeated with three different colonies, summing to a total sample size of 180 bees (26 were excluded later as result of infection by Deformed Wing Virus, see below).

tag: challenge

value: C

tag: time

tag: colony

tag: pair

tag: replicate

tag: index

value: TAATGCGC-TAATCTTA

tag: lane


title: C_60m_cR03_p01_50_GAATTCGT-CAGGACGT_L00M_R1_001

value: GAATTCGT-CAGGACGT


title: C_60m_cR02_p10_43_TCCGGAGA-ATAGAGGC_L00M_R1_001

value: TCCGGAGA-ATAGAGGC


title: C_60m_cR02_p09_42_TCCGGAGA-TATAGCCT_L00M_R1_001

description: excluded from analysis due to high DWV content

value: TCCGGAGA-TATAGCCT


title: SAM24294905 Intestine Small S2_EpCAM_48h bulk AKVPL 48h Saline

description:
timepoint: 48h
treatment_name: Saline


title: hESC-7

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

country: China

institute: Liangzhu Laboratory

description: Chemical labeled genomic DNA

library_source: genomic

data_processing:
Library strategy: 5-formylcytosine-seq
Illumina CASAVA version 1.8 were used to the basecalling.
All the de-multiplexed fastq reads were stripped to remove the low-quality bases and artificial sequences, including MALBAC primer and illumina adapter sequences using trim galore (version: 0.3.3) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and customized scripts.
The remaining cleaned reads were then aligned to the mm9 mouse reference genome (downloaded from the UCSC Genome Browser) using the Bismark tool (version: 0.13) (http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/) with the default parameters(Krueger and Andrews, 2011). Duplicated reads were removed using samtools (version: 0.1.18) (http://samtools.sourceforge.net/). The 5fC site identification was performed using customized scripts.
Genome_build: mm9,hg19
Supplementary_files_format_and_content: The processed file (in compressed bed format) includes the chromosome start position, chromasome end position of each covered cytosine, "0" refers to the regular cytosine, "1" refers to 5fC site; while "+" represents the plus strand, "-" represents minus strand, respectively.

molecule: genomic DNA

source_name: human embyro stem cell

extract_protocol:
Single mouse/human embryonic stem cells, gametes and early embryos were picked into the lysis buffer (20 mMTris, 2 mM EDTA, 20 mMKCl, and 0.3% TritonX-100) using a mouth pipette. Genomic DNAs were released after treatment with proteinase (QIAGEN) at 50°C for 3 h.
To label the 5fC adequately, 150 mMmalononitrile (J&K) was added directly to the single cell lysate, which was allowed to react at 37°C for 20 h with continuously shaking in a thermomixer (Eppendorf, 850 r.p.m.). To obtain the whole genome 5fC profiles from the single cells, MALBAC technique was applied to amplify the malononitrile-labeled genomic DNAs with minor modifications(Zong et al., 2012). Briefly, 11 rounds of quasi-linear pre-amplification and 15 cycles of exponential amplification were performed to obtain sufficient DNA for library construction. Sequencing libraries were constructed under the instruction of NEBNext Ultra DNA Library Prep Kit for Illumina (NEB), and the final libraries were amplified using the DeepVent DNA polymerase (3’-5’ exo-, NEB).

tag: cell type

value: human ESC

tag: gender

value: female

tag: strain

tag: development stage

value: inner cell mass

tag: bulk or single cell

value: single cell


title: C_60m_cR02_p08_39_AGCGATAG-GTACTGAC_L006_R1_001

value: AGCGATAG-GTACTGAC


title: hESC-8

description: Chemical labeled genomic DNA


title: C_60m_cR02_p05_31_AGCGATAG-AGGCGAAG_L005_R1_001

value: AGCGATAG-AGGCGAAG


title: C_60m_cR02_p06_35_AGCGATAG-TAATCTTA_L005_R1_001

value: AGCGATAG-TAATCTTA


title: D3_Ezh2_cKO

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description: Barcode: IATCACG

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: Immature mouse chondrocytes

growth_protocol: Chondrocytes were isolated from the femoral head, femoral condyles and tibial plateau as previously described (Gosset et al 2008). Chondrocytes were maintained in DMEM 2% FBS, 1% anti-mycotic/antibiotic.

extract_protocol:
IMC were isolated at days 3, 7, and 14 of culture. Micromasses were washed with PBS and mechanically disrupted with a scalpel, and Qiazol was added to lyse cells. Total RNA was extracted using the miRNeasy MicroKit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wildtype and Ezh2-deficient chondrocytes were differentiated micromass culture in growth media supplemented with Insulin-Transferrin-Selenium solution, 0.05mg/mL ascorbic acid and 10mM β-glycerol phosphate.

value: C57BL/6 - mix

tag: genotype/variation

tag: age

value: post-natal day 5

value: Immature mouse chondrocytes

value: day 3 of differentiation


title: hESC-5

description: Chemical labeled genomic DNA


title: C_60m_cR02_p04_30B_AGCGATAG-GGCTCTGA_L004_R1_001

value: AGCGATAG-GGCTCTGA


title: C_60m_cR02_p02_26_AGCGATAG-ATAGAGGC_L003_R1_001

value: C

value: AGCGATAG-ATAGAGGC


title: C_60m_cR02_p01_23_AGCGATAG-TATAGCCT_L003_R1_001

value: AGCGATAG-TATAGCCT


title: C_60m_cR02_p03_28_AGCGATAG-CCTATCCT_L004_R1_001

value: AGCGATAG-CCTATCCT


title: hESC-1

description: Chemical labeled genomic DNA


title: hESC-3

description: Chemical labeled genomic DNA


title: TE-05

description: Chemical labeled genomic DNA

source_name: trophectoderm

value: TE

value: trophectoderm


title: hESC-10

description: Chemical labeled genomic DNA

value: human ESC

value: female


title: C_30m_cR21_p08_14_TCCGGAGA-GTACTGAC_L002_R1_001

value: TCCGGAGA-GTACTGAC


title: hESC-9

description: Chemical labeled genomic DNA

value: inner cell mass

value: single cell


title: C_30m_cR21_p10_18_GAGATTCC-ATAGAGGC_L002_R1_001

value: GAGATTCC-ATAGAGGC


title: C_30m_cR21_p06_12B_TCCGGAGA-TAATCTTA_L006_R1_001

value: TCCGGAGA-TAATCTTA


title: hESC-2

description: Chemical labeled genomic DNA


title: C_30m_cR21_p07_13_TCCGGAGA-CAGGACGT_L001_R1_001

value: TCCGGAGA-CAGGACGT


title: TE-02

description: Chemical labeled genomic DNA


title: TE-04

description: Chemical labeled genomic DNA


title: hESC-6

description: Chemical labeled genomic DNA


title: C_30m_cR21_p05_8B_TCCGGAGA-AGGCGAAG_L005_R1_001

value: TCCGGAGA-AGGCGAAG


title: C_30m_cR21_p04_7_TCCGGAGA-GGCTCTGA_L004_R1_001

value: TCCGGAGA-GGCTCTGA


title: C_30m_cR21_p02_2_TCCGGAGA-ATAGAGGC_L002_R1_001

value: TCCGGAGA-ATAGAGGC


title: mESC(serum)-07

description: Chemical labeled genomic DNA

source_name: mouse embyro stem cell(serum)

value: mouse ESC(serum)


title: TE-01

description: Chemical labeled genomic DNA


title: C_30m_cR21_p01_1_TCCGGAGA-TATAGCCT_L00M_R1_001

value: C

value: TCCGGAGA-TATAGCCT


title: hESC-4

description: Chemical labeled genomic DNA


title: mESC(serum)-08

description: Chemical labeled genomic DNA


title: C_30m_cR03_p10_67_GAATTCGT-TAATCTTA_L00M_R1_001

value: GAATTCGT-TAATCTTA


title: C_30m_cR21_p09_16_GAGATTCC-TATAGCCT_L001_R1_001

value: GAGATTCC-TATAGCCT


title: C_60m_cR02_p07_38B_AGCGATAG-CAGGACGT_L006_R1_001

value: AGCGATAG-CAGGACGT


title: mESC(serum)-05

description: Chemical labeled genomic DNA


title: mESC(serum)-06

description: Chemical labeled genomic DNA


title: mESC(serum)-04

description: Chemical labeled genomic DNA


title: mESC(serum)-03

description: Chemical labeled genomic DNA


title: C_30m_cR03_p09_66_GAATTCGT-AGGCGAAG_L00M_R1_001

value: GAATTCGT-AGGCGAAG


title: mESC(serum)-01

description: Chemical labeled genomic DNA


title: TE-03

description: Chemical labeled genomic DNA

value: TE

value: trophectoderm


title: mESC(serum)-02

description: Chemical labeled genomic DNA

value: inner cell mass


title: C_30m_cR03_p08_63_GAATTCGT-GGCTCTGA_L00M_R1_001

value: GAATTCGT-GGCTCTGA


title: C_30m_cR03_p07_61_GAATTCGT-CCTATCCT_L00M_R1_001

value: GAATTCGT-CCTATCCT


title: ICM-09

description: Chemical labeled genomic DNA

source_name: inner cell mass

value: ICM

value: single cell


title: C_30m_cR03_p05_58_GAATTCGT-TATAGCCT_L00M_R1_001

value: GAATTCGT-TATAGCCT


title: ICM-08

description: Chemical labeled genomic DNA


title: C_30m_cR03_p06_59_GAATTCGT-ATAGAGGC_L00M_R1_001

value: GAATTCGT-ATAGAGGC


title: ICM-07

description: Chemical labeled genomic DNA


title: C_30m_cR03_p04_55_GAGATTCC-GTACTGAC_L00M_R1_001

value: GAGATTCC-GTACTGAC


title: C_30m_cR21_p03_5_TCCGGAGA-CCTATCCT_L003_R1_001

value: TCCGGAGA-CCTATCCT


title: C_30m_cR03_p03_54_GAGATTCC-CAGGACGT_L00M_R1_001

value: C

value: GAGATTCC-CAGGACGT


title: ICM-04

description: Chemical labeled genomic DNA


title: C_30m_cR03_p02_53_GAGATTCC-TAATCTTA_L00M_R1_001

value: GAGATTCC-TAATCTTA


title: C_30m_cR03_p01_52_GAGATTCC-AGGCGAAG_L00M_R1_001

value: GAGATTCC-AGGCGAAG


title: C_30m_cR02_p10_43_TCCGCGAA-GTACTGAC_L006_R1_001

value: TCCGCGAA-GTACTGAC


title: ICM-06

description: Chemical labeled genomic DNA


title: C_30m_cR02_p09_40_TCCGCGAA-CAGGACGT_L006_R1_001

value: TCCGCGAA-CAGGACGT


title: ICM-02

description: Chemical labeled genomic DNA


title: C_30m_cR02_p08_38_TCCGCGAA-TAATCTTA_L005_R1_001

value: TCCGCGAA-TAATCTTA


title: ICM-01

description: Chemical labeled genomic DNA


title: C_30m_cR02_p06_35_TCCGCGAA-GGCTCTGA_L004_R1_001

value: TCCGCGAA-GGCTCTGA


title: ICM-05

description: Chemical labeled genomic DNA

value: inner cell mass


title: C_30m_cR02_p05_34_TCCGCGAA-CCTATCCT_L004_R1_001

value: TCCGCGAA-CCTATCCT


title: EpiSC-09

description: Chemical labeled genomic DNA

source_name: Epiblast stem cell

value: EpiSC

value: epiblast


title: C_30m_cR02_p03_29_TCCGCGAA-TATAGCCT_L003_R1_001

value: TCCGCGAA-TATAGCCT


title: C_30m_cR02_p04_33p_TCCGCGAA-ATAGAGGC_L003_R1_001

value: TCCGCGAA-ATAGAGGC


title: EpiSC-05

description: Chemical labeled genomic DNA

value: single cell


title: EpiSC-06

description: Chemical labeled genomic DNA


title: C_30m_cR02_p01_26_TAATGCGC-CAGGACGT_L001_R1_001

value: TAATGCGC-CAGGACGT


title: C_30m_cR02_p02_27_TAATGCGC-GTACTGAC_L002_R1_001

value: TAATGCGC-GTACTGAC


title: EpiSC-07

description: Chemical labeled genomic DNA


title: X_30m_cR02_p05_34_CGGCTATG-CCTATCCT_L004_R1_001

value: X

value: CGGCTATG-CCTATCCT


title: EpiSC-04

description: Chemical labeled genomic DNA


title: C_120m_cR21_p10_17_TAATGCGC-TAATCTTA_L006_R1_001

value: C

value: TAATGCGC-TAATCTTA


title: C_120m_cR21_p09_16_TAATGCGC-AGGCGAAG_L005_R1_001

value: TAATGCGC-AGGCGAAG


title: C_120m_cR21_p08_13_TAATGCGC-GGCTCTGA_L004_R1_001

value: TAATGCGC-GGCTCTGA


title: EpiSC-02

description: Chemical labeled genomic DNA


title: EpiSC-03

description: Chemical labeled genomic DNA


title: ICM-03

description: Chemical labeled genomic DNA

value: ICM


title: C_120m_cR21_p07_12_TAATGCGC-CCTATCCT_L003_R1_001

value: TAATGCGC-CCTATCCT


title: EpiSC-10

description: Chemical labeled genomic DNA


title: 4cell-02d

description: Chemical labeled genomic DNA


title: EpiSC-01

description: Chemical labeled genomic DNA


title: C_120m_cR21_p06_11_TAATGCGC-ATAGAGGC_L002_R1_001

value: TAATGCGC-ATAGAGGC


title: 4cell-02c

description: Chemical labeled genomic DNA


title: C_30m_cR02_p07_36p_TCCGCGAA-AGGCGAAG_L005_R1_001

value: TCCGCGAA-AGGCGAAG


title: 4cell-02b

description: Chemical labeled genomic DNA


title: C_120m_cR21_p05_10B_TAATGCGC-TATAGCCT_L001_R1_001

value: TAATGCGC-TATAGCCT


title: C_120m_cR21_p03_7B_GAATTCGT-CAGGACGT_L001_R1_001

value: GAATTCGT-CAGGACGT


title: EpiSC-08

description: Chemical labeled genomic DNA

value: EpiSC

value: epiblast


title: C_120m_cR21_p02_5_GAATTCGT-TAATCTTA_L006_R1_001

value: GAATTCGT-TAATCTTA


title: 4cell-02a

description: Chemical labeled genomic DNA

value: single cell


title: 4cell-01d

description: Chemical labeled genomic DNA


title: C_120m_cR03_p10_69_AGCGATAG-GTACTGAC_L001_R1_001

value: AGCGATAG-GTACTGAC


title: 4cell-01b

description: Chemical labeled genomic DNA


title: C_120m_cR03_p07_59B_TCCGCGAA-CAGGACGT_L00M_R1_001

value: TCCGCGAA-CAGGACGT


title: C_120m_cR03_p09_67B_AGCGATAG-CAGGACGT_L001_R1_001

value: AGCGATAG-CAGGACGT


title: 4cell-01a

description: Chemical labeled genomic DNA


title: C_120m_cR03_p08_64_AGCGATAG-TAATCTTA_L001_R1_001

value: C

value: AGCGATAG-TAATCTTA


title: C_120m_cR21_p01_3_GAATTCGT-AGGCGAAG_L005_R1_001

value: GAATTCGT-AGGCGAAG


title: 2cell-06b

description: Chemical labeled genomic DNA


title: 2cell-06a

description: Chemical labeled genomic DNA


title: 2cell-01b

description: Chemical labeled genomic DNA


title: C_120m_cR03_p06_57_TCCGCGAA-TAATCTTA_L00M_R1_001

value: TCCGCGAA-TAATCTTA


title: 2cell-08a

description: Chemical labeled genomic DNA


title: 2cell-01a

description: Chemical labeled genomic DNA


title: C_120m_cR03_p05_55_TCCGCGAA-AGGCGAAG_L00M_R1_001


title: C_120m_cR21_p04_8B_GAATTCGT-GTACTGAC_L002_R1_001

value: GAATTCGT-GTACTGAC


title: 2cell-05b

description: Chemical labeled genomic DNA


title: 2cell-07b

description: Chemical labeled genomic DNA


title: C_120m_cR03_p04_54_TCCGCGAA-GGCTCTGA_L00M_R1_001

value: TCCGCGAA-GGCTCTGA


title: 2cell-05a

description: Chemical labeled genomic DNA


title: C_120m_cR03_p02_51_TCCGCGAA-ATAGAGGC_L00M_R1_001

value: TCCGCGAA-ATAGAGGC


title: C_120m_cR02_p10_42_GAGATTCC-GGCTCTGA_L00M_R1_001

value: GAGATTCC-GGCTCTGA


title: C_120m_cR02_p09_39_GAGATTCC-CCTATCCT_L00M_R1_001

value: GAGATTCC-CCTATCCT


title: 2cell-07a

description: Chemical labeled genomic DNA


title: C_120m_cR03_p01_50_TCCGCGAA-TATAGCCT_L00M_R1_001

value: TCCGCGAA-TATAGCCT


title: 2cell-04b

description: Chemical labeled genomic DNA


title: 2cell-04a

description: Chemical labeled genomic DNA


title: C_120m_cR02_p07_32_GAGATTCC-TATAGCCT_L00M_R1_001

value: GAGATTCC-TATAGCCT


title: C_120m_cR02_p06_31B_TCCGGAGA-GTACTGAC_L00M_R1_001

value: TCCGGAGA-GTACTGAC


title: C_120m_cR02_p05_30_TCCGGAGA-CAGGACGT_L00M_R1_001

value: TCCGGAGA-CAGGACGT


title: 2cell-03a

description: Chemical labeled genomic DNA

value: single cell


title: Sperm-03

description: Chemical labeled genomic DNA

source_name: sperm

value: sperm

value: male


title: Sperm-R1

description: Chemical labeled genomic DNA

value: bulk


title: Sperm-07

description: Chemical labeled genomic DNA


title: C_120m_cR02_p03_26B_TCCGGAGA-AGGCGAAG_L00M_R1_001

value: C

value: TCCGGAGA-AGGCGAAG


title: C_120m_cR02_p02_25_TCCGGAGA-GGCTCTGA_L00M_R1_001

value: TCCGGAGA-GGCTCTGA


title: C_120m_cR03_p03_52_TCCGCGAA-CCTATCCT_L00M_R1_001

value: TCCGCGAA-CCTATCCT


title: C_120m_cR02_p01_21_TCCGGAGA-CCTATCCT_L00M_R1_001

value: TCCGGAGA-CCTATCCT


title: Sperm-01

description: Chemical labeled genomic DNA


title: Sperm-04

description: Chemical labeled genomic DNA


title: Sperm-02

description: Chemical labeled genomic DNA


title: Sperm-06

description: Chemical labeled genomic DNA


title: PaternalPN-11

description: Chemical labeled genomic DNA

source_name: Paternal pronuclei

value: Paternal pronuclei

value: zygote


title: C_120m_cR02_p04_29B_TCCGGAGA-TAATCTTA_L00M_R1_001

value: TCCGGAGA-TAATCTTA


title: Sperm-R2

description: Chemical labeled genomic DNA


title: PaternalPN-10

description: Chemical labeled genomic DNA


title: PaternalPN-06

description: Chemical labeled genomic DNA


title: PaternalPN-07

description: Chemical labeled genomic DNA


title: PaternalPN-04

description: Chemical labeled genomic DNA


title: MaternalPN-09

description: Chemical labeled genomic DNA

source_name: maternal pronuclei

value: maternal pronuclei

value: female


title: PaternalPN-03

description: Chemical labeled genomic DNA


title: PaternalPN-01

description: Chemical labeled genomic DNA


title: MaternalPN-10

description: Chemical labeled genomic DNA


title: MaternalPN-07

description: Chemical labeled genomic DNA


title: MaternalPN-08

description: Chemical labeled genomic DNA


title: MaternalPN-05

description: Chemical labeled genomic DNA


title: MaternalPN-06

description: Chemical labeled genomic DNA


title: MaternalPN-04

description: Chemical labeled genomic DNA


title: MaternalPN-02

description: Chemical labeled genomic DNA


title: MaternalPN-01

description: Chemical labeled genomic DNA


title: Sperm-05

description: Chemical labeled genomic DNA


title: AKVPSL_tumor

data_processing:
Library strategy: WGS
Reads were aligned to the GRCm38 genome using GSNAP version ‘2013-10-10’, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap’).
Copy number changes in each of the three genotypes were called by comparing their WGS data to the sequencing data from the spleen of the donor using Control-FREEC v9.9 with a window size of 50kb
Genome_build: GRCh38
Supplementary_files_format_and_content: text file for each organoid sample containing all windows along the genome and the inferred median ratio and copy number

source_name: Small Intestine

extract_protocol:
gDNA was extracted from each in vitro organoid culture, and spleen from AKVL donor animal, using DNeasy Blood and Tiissue kit (Qiagen) according to manufacture's recommendation
Whole genome sequencing libraries were prepared for sequencing using standard Illumina protocols

value: adenocarcinoma metastatic

tag: tissue

value: Small Intestine


title: AKVL_tumor  [exome-capture]

data_processing:
Library strategy: exome capture
Reads were aligned to the GRCm38 genome using GSNAP version ‘2013-10-10’, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap’).
Somatic single nucleotide variants (SNVs) and insertions/deletions (indels) were called using loFreq by comparing each of the three genotypes to the spleen
Genome_build: GRCm38
Supplementary_files_format_and_content: Two vcf files for each genotype containing SNVs and indels, respectively

extract_protocol:
gDNA was extracted from each in vitro organoid culture, and spleen from AKVL donor animal, using DNeasy Blood and Tiissue kit (Qiagen) according to manufacture's recommendation
Exome capture was performed using Agilent's SureSelect Mouse 50Mb baits and processed using the SureSelect V1.5.1 protocol

value: adenoma


title: AKVPL_tumor

value: carcinoma


title: AKVPSL_tumor  [exome-capture]


title: AKVPL_tumor  [exome-capture]


title: AKVL_spleen  [exome-capture]

source_name: Spleen

value: normal

value: Spleen


title: AKVL_spleen


title: SAM24294913 Intestine Small S2_EpCAM_96h bulk AKVPL 96h Saline

description:
timepoint: 96h
treatment_name: Saline

value: Intestine Small

tag: sort

value: bulk

value: AKVPL


title: PaternalPN-05

description: Chemical labeled genomic DNA

value: male

value: single cell


title: C_120m_cR02_p08_34_GAGATTCC-ATAGAGGC_L00M_R1_001

value: C

value: GAGATTCC-ATAGAGGC


title: SAM24294916 Intestine Small DT1_EpCAM_96h bulk AKVPL 96h DT

description:
timepoint: 96h
treatment_name: DT

tag: genotype


title: SAM24294912 Intestine Small S1_EpCAM_96h bulk AKVPL 96h Saline

description:
timepoint: 96h
treatment_name: Saline


title: SAM24294899 Intestine Small S4_EpCAM_24h bulk AKVPL 24h Saline

description:
timepoint: 24h
treatment_name: Saline


title: SAM24294896 Intestine Small S1_EpCAM_24h bulk AKVPL 24h Saline

description:
timepoint: 24h
treatment_name: Saline


title: SAM24294919 Intestine Small DT4_EpCAM_96h bulk AKVPL 96h DT

description:
timepoint: 96h
treatment_name: DT


title: SAM24294915 Intestine Small S4_EpCAM_96h bulk AKVPL 96h Saline

description:
timepoint: 96h
treatment_name: Saline


title: SAM24294898 Intestine Small S3_EpCAM_24h bulk AKVPL 24h Saline

description:
timepoint: 24h
treatment_name: Saline


title: SAM24294914 Intestine Small S3_EpCAM_96h bulk AKVPL 96h Saline

description:
timepoint: 96h
treatment_name: Saline


title: SAM24294903 Intestine Small DT4_EpCAM_24h bulk AKVPL 24h DT

description:
timepoint: 24h
treatment_name: DT


title: SAM24294900 Intestine Small DT1_EpCAM_24h bulk AKVPL 24h DT

description:
timepoint: 24h
treatment_name: DT


title: MaternalPN-03

description: Chemical labeled genomic DNA

value: zygote


title: SAM24294917 Intestine Small DT2_EpCAM_96h bulk AKVPL 96h DT

description:
timepoint: 96h
treatment_name: DT


title: SAM24294918 Intestine Small DT3_EpCAM_96h bulk AKVPL 96h DT

description:
timepoint: 96h
treatment_name: DT


title: SAM24294897 Intestine Small S2_EpCAM_24h bulk AKVPL 24h Saline

description:
timepoint: 24h
treatment_name: Saline


title: Lgr5+ intestinal_stem_cells_rep3 (rnaseq)

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with STAR_2.3.1z13_r470 onto the iGenomes mm9 reference
Secondary alignments were filtered with samtools 1.2
Counts for every gene were calculated with HTSeq-0.6.1p1 using the gene model provided with the iGenomes mm9 reference from 2013-03-06
Counts were normalized and modeled with DESeq2_1.6.3
Genome_build: mm9
Supplementary_files_format_and_content: tab separated file containing counts per gene

source_name: Lgr5+ intestinal stem cells from adult mice

extract_protocol:
[Samples E14.5 and E12.5] Fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS directly in 300 ml of RTL buffer (Qiagen) supplemented with 1% b-mercaptoethanol and stored at -80°C. For each replicate, RNA was isolated from pools of 20 embryos (E12.5) or one adult gut using RNeasy micro-kit (Qiagen).
[Samples AE and ISC] Fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS directly in 300 ml of RTL buffer (Qiagen) supplemented with 1% b-mercaptoethanol and stored at -80°C. For each replicate, RNA was isolated from pools of 20 embryos (E12.5) or one adult gut using RNeasy micro-kit (Qiagen).
50ng of total RNA was used for cDNA synthesis using Ovation v2.0 kit (NuGEN) according to manufacturer’s instructions. After cDNA fragmentation (Covaris), libraries were prepared using NEBNext v2.0 kit (NEB) according to manufacturer’s instructions.

treatment_protocol:
[Samples E14.5 and E12.5] Small intestines were dissected from mouse embryos at indicated stages, cut in pieces of 2 mm and incubated for 5-10 min with 0.15mg/ml collagenase (Sigma) in PBS at 37°C with shaking at 800 rpm. Single cell suspensions were collected by centrifugation at 200g for 3 min, washed twice and resuspended in PBS supplemented with 2% foetal calf serum. Cells were stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 15 min at room temperature. Living cells were gated by DAPI dye exclusion. Embryonic intestinal epithelial cells were isolated as EpCAM+CD31−CD45−DAPI−. Fluorescence-activated cell sorting was performed using BD FACS Aria III SORP cell sorter (85 μM nozzle)
[Samples AE and ISC] Small intestines were dissected from 2 months old Lgr5EGFP-Cre-ERT males, cut in pieces of 2 mm2, placed into 50 ml conical tubes and washed 3 times for 10 min with 40 ml of PBS/ 5 mM EDTA on a rocking plate at room temperature. Villi were mechanically removed by gentle shaking 3 times and trituration using a 10 ml pipette. Villi material was collected by centrifugation at 200g for 3 min and washed twice with PBS. Crypts were separated from the intestine by vigorous shaking 2 times passing through a 70μM filter (BD Falcon). Crypt material was collected by centrifugation at 200g for 3 min, washed twice with PBS and incubated for 5-10 min with 0.15 mg/ml collagenase (Sigma) and 0.1 mg/ml DNase I (Qiagen) at 37°C on a rocking plate. Single cell suspensions were washed twice and resuspended in PBS supplemented with 2% foetal calf serum. Cells were stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 30 min at room temperature. Living cells were gated by DAPI dye exclusion. Enterocytes were isolated as EpCAM+CD31−CD45−DAPI−. ISCs were isolated as Lgr5-EGFPhighCD31−CD45−DAPI−. Fluorescence-activated cell sorting was performed using BD FACS Aria III SORP cell sorter (85 μM nozzle)

value: mixed C57BL/6 CD1

value: small intestine

value: Lgr5+ intestinal stem cell


title: SAM24294901 Intestine Small DT2_EpCAM_24h bulk AKVPL 24h DT

description:
timepoint: 24h
treatment_name: DT


title: Lgr5+ intestinal_stem_cells_rep1 (rnaseq)


title: Lgr5+ intestinal_stem_cells_rep2 (rnaseq)


title: AKVL_tumor


title: SAM24294902 Intestine Small DT3_EpCAM_24h bulk AKVPL 24h DT

description:
timepoint: 24h
treatment_name: DT


title: embryo_14.5_days_rep3 (rnaseq)

source_name: EpCAM+ epithelium from small intestine

value: intestinal epithelial cell


title: embryo_14.5_days_rep2 (rnaseq)


title: embryo_14.5_days_rep1 (rnaseq)


title: embryo_12.5_days_rep3 (rnaseq)


title: embryo_12.5_days_rep1 (rnaseq)


title: embryo_12.5_days_rep2 (rnaseq)


title: adult_enterocytes_rep1 (rnaseq)

source_name: enterocyte from adult mice

value: enterocyte


title: adult_enterocytes_rep2 (rnaseq)


title: adult_enterocytes_rep3 (rnaseq)


title: embryo_14.5_days_rep2 (mbd)

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with Bowtie 1.1.2 onto the iGenomes mm9 reference
Secondary alignments were filtered with samtools 1.2
Peaks called with Macs 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: tab separated file containing peaks called by macs with the following columns: chr, start, end, length, summit, tags, -10*log10(pvalue), fold_enrichment

extract_protocol:
[Samples E14.5 and E12.5] Two hundred thousand EpCAM+ embryonic intestinal cells were isolated by FACS and stored at -80°C. For each replicate, DNA was isolated using phenol: chloroform extraction. 1 ug of genomic DNA was fragmented to 150-250 bp using Covaris. MBD pull-downs were performed using Methylminer Methylated DNA Enrichment kit (Invitrogen) according to manufacturer’s instructions.
[Samples AE and ISC] Two hundred thousand Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS and stored at -80°C. For each replicate, DNA was isolated using phenol: chloroform extraction. 1 ug of genomic DNA was fragmented to 150-250 bp using Covaris. MBD pull-downs were performed using Methylminer Methylated DNA Enrichment kit (Invitrogen) according to manufacturer’s instructions.
Libraries were prepared using NEBNext v2.0 kit (NEB) according to manufacturer’s instructions.


title: Lgr5+ intestinal_stem_cells_rep1 (mbd)


title: embryo_12.5 days_rep2 (mbd)


title: adult_enterocytes_rep2 (mbd)


title: embryo_12.5 days_rep1 (mbd)


title: adult_enterocytes_rep1 (mbd)


title: embryo_14.5_days_input (k27m3)

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with Bowtie 1.1.2 onto the iGenomes mm9 reference
Secondary alignments were filtered with samtools 1.2
Peaks were called with SICER 1.1 with window size=200, gap_size=1000 and FDR=0.01
Genome_build: mm9
Supplementary_files_format_and_content: tab separated file containing peaks called by SICER, with the following columns: chr, start, end, peak length, summit, pvalue, enrichment over the input, fdr

extract_protocol:
[Samples E14.5 and E12.5] Single cell suspensions of embryonic cells were fixed for 10 min with 1% PFA at RT, washed twice with PBS and stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 15-30 min at RT. Two hundred fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS and stored at -80°C. To obtain fragments around 350-700 bp, chromatin was resuspended in 150 uL of sonication buffer (1% SDS, 50 mM Tris-Cl pH 8.0, 10 mM EDTA) and sonicated for 56 cycles 10 sec ON/ 90 sec OFF (Diagenode) at 4C.H3K27me3 (Millipore #17-622) antibodies were used. 20 uL of Protein A/G sepharose beads (Sigma, P6486 and E3403) were pre-incubated for 3 hours with 0.5 ug of antibody in RIPA buffer, then washed3 times with RIPA buffer. The sonicated chromatin was diluted till final volume 750 uL and incubated with antibody-bead slurry at 4C overnight. Beads were washed 3 times with 1 mL of RIPA buffer and once with TE. DNA was eludet and incubated with RNAse A for 30 min, followed by ON incubation with PK. DNA was extracted using phenol: chloroform.
[Samples AE and ISC] Single cell suspensions of adult cells were fixed for 10 min with 1% PFA at RT, washed twice with PBS and stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 15-30 min at RT. Two hundred fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS and stored at -80°C. To obtain fragments around 350-700 bp, chromatin was resuspended in 150 uL of sonication buffer (1% SDS, 50 mM Tris-Cl pH 8.0, 10 mM EDTA) and sonicated for 56 cycles 10 sec ON/ 90 sec OFF (Diagenode) at 4C. H3K27me3 (Millipore #17-622) antibodies were used. 20 uL of Protein A/G sepharose beads (Sigma, P6486 and E3403) were pre-incubated for 3 hours with 0.5 ug of antibody in RIPA buffer, then washed3 times with RIPA buffer. The sonicated chromatin was diluted till final volume 750 uL and incubated with antibody-bead slurry at 4C overnight. Beads were washed 3 times with 1 mL of RIPA buffer and once with TE. DNA was eludet and incubated with RNAse A for 30 min, followed by ON incubation with PK. DNA was extracted using phenol: chloroform.
Libraries were prepared using NuGEN Ovation Ultralow Library System V2 (NuGEN) according to manufacturer’s instructions.

tag: chip antibody


title: Lgr5+ intestinal_stem_cells_rep2 (k27m3)

value: H3K27me3:Millipore #17-622


title: Lgr5+ intestinal_stem_cells_rep1 (k27m3)


title: embryo_12.5 days_input (k27m3)


title: embryo_14.5_days_rep1 (k27m3)


title: embryo_12.5 days_rep2 (k27m3)


title: embryo_14.5_days_rep1 (mbd)


title: embryo_12.5 days_rep1 (k27m3)


title: adult_enterocytes_input (k27m3)


title: adult_enterocytes_rep1 (k27m3)


title: Lgr5+ intestinal_stem_cells_rep2 (mbd)


title: Lgr5+ intestinal_stem_cells_rep1_input (k27ac)

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with Bowtie 1.1.2 onto the iGenomes mm9 reference
Secondary alignments were filtered with samtools 1.2
Peaks were called with Macs 2.1.0.20140616 with -m 10 30 -g mm --bw 200
Genome_build: mm9
Supplementary_files_format_and_content: tab separated file containing peaks called by macs2 (XLS macs2 format) with the following columns: chr, start, end, length, abs_summit, pileup, -log10(pvalue), fold_enrichment, -log10(qvalue), name

extract_protocol:
[Samples E14.5 and E12.5] Single cell suspensions of embryonic cells were fixed for 10 min with 1% PFA at RT, washed twice with PBS and stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 15-30 min at RT. Two hundred fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS and stored at -80°C. To obtain fragments around 350-700 bp, chromatin was resuspended in 150 uL of sonication buffer (1% SDS, 50 mM Tris-Cl pH 8.0, 10 mM EDTA) and sonicated for 56 cycles 10 sec ON/ 90 sec OFF (Diagenode) at 4C. H3K27Ac (Abcam 4729) antibodies were used. 20 uL of Protein A/G sepharose beads (Sigma, P6486 and E3403) were pre-incubated for 3 hours with 0.5 ug of antibody in RIPA buffer, then washed3 times with RIPA buffer. The sonicated chromatin was diluted till final volume 750 uL and incubated with antibody-bead slurry at 4C overnight. Beads were washed 3 times with 1 mL of RIPA buffer and once with TE. DNA was eludet and incubated with RNAse A for 30 min, followed by ON incubation with PK. DNA was extracted using phenol: chloroform.
[Samples AE and ISC] Single cell suspensions of adult cells were fixed for 10 min with 1% PFA at RT, washed twice with PBS and stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 15-30 min at RT. Two hundred fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS and stored at -80°C. To obtain fragments around 350-700 bp, chromatin was resuspended in 150 uL of sonication buffer (1% SDS, 50 mM Tris-Cl pH 8.0, 10 mM EDTA) and sonicated for 56 cycles 10 sec ON/ 90 sec OFF (Diagenode) at 4C. H3K27Ac (Abcam 4729) antibodies were used. 20 uL of Protein A/G sepharose beads (Sigma, P6486 and E3403) were pre-incubated for 3 hours with 0.5 ug of antibody in RIPA buffer, then washed3 times with RIPA buffer. The sonicated chromatin was diluted till final volume 750 uL and incubated with antibody-bead slurry at 4C overnight. Beads were washed 3 times with 1 mL of RIPA buffer and once with TE. DNA was eludet and incubated with RNAse A for 30 min, followed by ON incubation with PK. DNA was extracted using phenol: chloroform.
Libraries were prepared using NuGEN Ovation Ultralow Library System V2 (NuGEN) according to manufacturer’s instructions.


title: Lgr5+ intestinal_stem_cells_rep2_input (k27ac)


title: Lgr5+ intestinal_stem_cells_rep1 (k27ac)

value: H3K27Ac:Abcam 4729


title: Lgr5+ intestinal_stem_cells_rep2 (k27ac)


title: Lgr5+ intestinal_stem_cells_input (k27m3)


title: embryo_14.5_days_rep2_input (k27ac)


title: embryo_14.5_days_rep2 (k27ac)


title: embryo_14.5_days_rep1_input (k27ac)


title: embryo_12.5 days_rep1_input (k27ac)


title: embryo_14.5_days_rep1 (k27ac)


title: embryo_12.5 days_rep1 (k27ac)


title: embryo_14.5_days_rep2 (k27m3)


title: embryo_12.5 days_rep2_input (k27ac)


title: adult_enterocytes_rep2 (k27ac)


title: adult_enterocytes_rep1 (k27ac)


title: adult_enterocytes_rep2 (k27m3)


title: Lgr5+ intestinal_stem_cells_input (k4m3)

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with Bowtie 1.1.2 onto the iGenomes mm9 reference
Secondary alignments were filtered with samtools 1.2
Peaks were called with Macs 2.1.0.20140616 with parameters -m 5 50 -g mm --broad
Genome_build: mm9
Supplementary_files_format_and_content: tab separated file containing peaks called by macs2 (XLS macs2 format) with the following columns: chr, start, end, length, pileup, -log10(pvalue), fold_enrichment, -log10(qvalue), name

extract_protocol:
[Samples E14.5 and E12.5] Single cell suspensions of embryonic cells were fixed for 10 min with 1% PFA at RT, washed twice with PBS and stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 15-30 min at RT. Two hundred fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS and stored at -80°C. To obtain fragments around 350-700 bp, chromatin was resuspended in 150 uL of sonication buffer (1% SDS, 50 mM Tris-Cl pH 8.0, 10 mM EDTA) and sonicated for 56 cycles 10 sec ON/ 90 sec OFF (Diagenode) at 4C. H3K4me3 (Millipore #07-473) antibodies were used. 20 uL of Protein A/G sepharose beads (Sigma, P6486 and E3403) were pre-incubated for 3 hours with 0.5 ug of antibody in RIPA buffer, then washed3 times with RIPA buffer. The sonicated chromatin was diluted till final volume 750 uL and incubated with antibody-bead slurry at 4C overnight. Beads were washed 3 times with 1 mL of RIPA buffer and once with TE. DNA was eludet and incubated with RNAse A for 30 min, followed by ON incubation with PK. DNA was extracted using phenol: chloroform.
[Samples AE and ISC] Single cell suspensions of adult cells were fixed for 10 min with 1% PFA at RT, washed twice with PBS and stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 15-30 min at RT. Two hundred fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS and stored at -80°C. To obtain fragments around 350-700 bp, chromatin was resuspended in 150 uL of sonication buffer (1% SDS, 50 mM Tris-Cl pH 8.0, 10 mM EDTA) and sonicated for 56 cycles 10 sec ON/ 90 sec OFF (Diagenode) at 4C. H3K4me3 (Millipore #07-473) antibodies were used. 20 uL of Protein A/G sepharose beads (Sigma, P6486 and E3403) were pre-incubated for 3 hours with 0.5 ug of antibody in RIPA buffer, then washed3 times with RIPA buffer. The sonicated chromatin was diluted till final volume 750 uL and incubated with antibody-bead slurry at 4C overnight. Beads were washed 3 times with 1 mL of RIPA buffer and once with TE. DNA was eludet and incubated with RNAse A for 30 min, followed by ON incubation with PK. DNA was extracted using phenol: chloroform.
Libraries were prepared using NuGEN Ovation Ultralow Library System V2 (NuGEN) according to manufacturer’s instructions.


title: embryo_14.5_days_input (k4m3)


title: embryo_12.5 days_input (k4m3)


title: embryo_14.5_days_rep1 (k4m3)

value: H3K4me3:Millipore #07-473


title: embryo_14.5_days_rep2 (k4m3)


title: embryo_12.5 days_rep2 (k4m3)


title: embryo_12.5 days_rep1 (k4m3)


title: Lgr5+ intestinal_stem_cells_rep2 (k4m3)


title: adult_enterocytes_input (k4m3)


title: adult_enterocytes_rep1 (k4m3)


title: adult_enterocytes_rep2 (k4m3)


title: Lgr5+ intestinal_stem_cells_input (h2az)

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with Bowtie 1.1.2 onto the iGenomes mm9 reference
Secondary alignments were filtered with samtools 1.2
Peaks were called with Macs 2.1.0.20140616 with parameters -m 10 30 -g mm --broad
Genome_build: mm9
Supplementary_files_format_and_content: tab separated file containing peaks called by macs2 (XLS macs2 format) with the following columns: chr, start, end, length, pileup, -log10(pvalue), fold_enrichment, -log10(qvalue), name

extract_protocol:
[Samples E14.5 and E12.5] Single cell suspensions of embryonic cells were fixed for 10 min with 1% PFA at RT, washed twice with PBS and stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 15-30 min at RT. Two hundred fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS and stored at -80°C. To obtain fragments around 350-700 bp, chromatin was resuspended in 150 uL of sonication buffer (1% SDS, 50 mM Tris-Cl pH 8.0, 10 mM EDTA) and sonicated for 56 cycles 10 sec ON/ 90 sec OFF (Diagenode) at 4C. H2A.Z (Active Motif, #39113) antibodies were used. 20 uL of Protein A/G sepharose beads (Sigma, P6486 and E3403) were pre-incubated for 3 hours with 0.5 ug of antibody in RIPA buffer, then washed3 times with RIPA buffer. The sonicated chromatin was diluted till final volume 750 uL and incubated with antibody-bead slurry at 4C overnight. Beads were washed 3 times with 1 mL of RIPA buffer and once with TE. DNA was eludet and incubated with RNAse A for 30 min, followed by ON incubation with PK. DNA was extracted using phenol: chloroform.
[Samples AE and ISC] Single cell suspensions of adult cells were fixed for 10 min with 1% PFA at RT, washed twice with PBS and stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 15-30 min at RT. Two hundred fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS and stored at -80°C. To obtain fragments around 350-700 bp, chromatin was resuspended in 150 uL of sonication buffer (1% SDS, 50 mM Tris-Cl pH 8.0, 10 mM EDTA) and sonicated for 56 cycles 10 sec ON/ 90 sec OFF (Diagenode) at 4C. H2A.Z (Active Motif, #39113) antibodies were used. 20 uL of Protein A/G sepharose beads (Sigma, P6486 and E3403) were pre-incubated for 3 hours with 0.5 ug of antibody in RIPA buffer, then washed3 times with RIPA buffer. The sonicated chromatin was diluted till final volume 750 uL and incubated with antibody-bead slurry at 4C overnight. Beads were washed 3 times with 1 mL of RIPA buffer and once with TE. DNA was eludet and incubated with RNAse A for 30 min, followed by ON incubation with PK. DNA was extracted using phenol: chloroform.
Libraries were prepared using NuGEN Ovation Ultralow Library System V2 (NuGEN) according to manufacturer’s instructions.


title: Lgr5+ intestinal_stem_cells_rep2 (h2az)

value: H2A.Z:Active Motif, #39113


title: Lgr5+ intestinal_stem_cells_rep1 (h2az)


title: embryo_12.5 days_rep2 (k27ac)


title: embryo_12.5 days_rep2_input (h2az)


title: embryo_14.5_days_rep1 (h2az)


title: embryo_12.5 days_rep2 (h2az)


title: embryo_14.5_days_rep2 (h2az)


title: embryo_12.5 days_rep1_input (h2az)


title: embryo_14.5_days_rep1_input (h2az)


title: adult_enterocytes_rep1_input (k27ac)


title: Lgr5+ intestinal_stem_cells_rep1 (k4m3)


title: embryo_12.5 days_rep1 (h2az)


title: adult_enterocytes_input (h2az)


title: adult_enterocytes_rep2 (h2az)


title: adult_enterocytes_rep1 (h2az)


title: shCUX1.810.rep3_RNA-seq

city: Chicago

first: Megan

middle: E.

last: McNerney

state: Illinois

address: 900 East 57th Street, KCBD 5128

department: Pathology

institute: The University of Chicago

description:
processed data file:
EdgeRResults.txt

data_processing:
RNA-seq reads were aligned to hg19 with Tophat .2.10 using default parameters. Reads with quality scores >30 were counted using HTseq-tools and analyzed with EdgeR
ChIP-seq reads were aligned to hg19 using bwa (version 0.7.5) and peaks called using Q.
Genome_build: Hg19
Supplementary_files_format_and_content: RNA-seq text file contains EdgeR results for Gene ID, log fold change, log counts per million, p value and q values for control versus knockdown.  ChIP-seq text file contains DiffBind results for peak location, mean occupancy in the control, mean ocupancy in the knockdown, fold change in occupancy, p value, and FDR for control versus knockdown.

organism: Homo sapiens

growth_protocol: K562 cells were grown in RPMI with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
RNA was isolated using Trizol. Genomic DNA was isolated follwing the Myers Lab ChIP-seq Protocol v042211.2 (www.encodeproject.org),
Barcoded RNA-seq libraries were generated using the standard Illumina TruSEQ kit. Barcoded ChIP-seq libraries were made with Ovation Ultralow Library kit (NuGEN).

treatment_protocol: For RNA-seq experiments, cells were treated with 2 ug/mL of doxycycline for four days.

tag: cell line

value: myeloid leukemia cell line

tag: shRNA

tag: chip-antibody


title: shCUX1.338.rep3_RNA-seq

description:
processed data file:
EdgeRResults.txt


title: shRen.rep3_RNA-seq

description:
processed data file:
EdgeRResults.txt

value: shRenilla


title: shRen.rep2_RNA-seq

description:
processed data file:
EdgeRResults.txt


title: B3-Normal-#2-1200cells

city: Boston

first: Xiaoji

last: Wu

state: MA

address: 149G Warren Alpert Building, 200 Longwood Avenue

department: PCMM

institute: Boston Children's Hospital

description: Batch 3, mouse 1, normal

data_processing:
Reads were trimmed and aligned using the drop-seq data analysis package.
Raw count for each gene was converted to TPM (transcript per million).
Genome_build: mm9
Supplementary_files_format_and_content: The processed txt files are tab-delimited count data for each gene of each single cell.
1443737Cells.SVM.cluster.identity.renamed.csv: Comma-separated text file documents cluster identity for each single cell.
1443737Cells.Expresssion.Matrix.log_tpm+1_.renamed.RData: Single-cell gene expression matrix in Rdata format.
Merged_17samples_14437cells_count.txt: Drop-seq count for 14437 cells from 17 samples

growth_protocol: Mice were maintained following the guidelines of the Institutional Animal Care and Use Committee at Harvard Medical School.

extract_protocol:
Hypothalamus was dissected and dissociated into single-cell suspension, followed by drop-seq library preparation.
Libraries were prepared following the protocol of drop-seq.

treatment_protocol: Mice were either fed normally or placed under food deprivation for 24 hours.

tag: batch no.

value: Batch 3

tag: strain background

value: B6D2F1 (C57BL6 female X DBA2 male)

tag: mouse id

value: mouse 1

tag: mouse status

value: normal

value: hypothalamus


title: embryo_14.5_days_rep2_input (h2az)

tag: cell type


title: B2-FD-#3-2200cells

description: Batch 2, mouse 2, food deprived

source_name: food deprived_hypothalamus

value: Batch 2

value: mouse 2

value: food deprived


title: B2-normal-#2-1200cells

description: Batch 2, mouse 1, normal


title: shCUX1.338.rep1_RNA-seq

description:
processed data file:
EdgeRResults.txt


title: B2-normal-#1-1200cells

description: Batch 2, mouse 1, normal


title: B2-FD-#2-400cells

description: Batch 2, mouse 2, food deprived


title: shRen.rep1_RNA-seq

description:
processed data file:
EdgeRResults.txt


title: B4-FD-#1-2200cells

description: Batch 4, mouse 1, food deprived

value: Batch 4


title: B2-FD-#1-1100cells

description: Batch 2, mouse 2, food deprived


title: B1-normal-#3-800cells

description: Batch 1, mouse 2, normal

value: Batch 1


title: B1-normal-#1-1200cells

description: Batch 1, mouse 2, normal


title: B1-FD-#3-1200cells

description: Batch 1, mouse 1, food deprived


title: B1-normal-#2-1000cells

description: Batch 1, mouse 2, normal


title: PROseq_macrophage2

city: Palo Alto

first: Kevin

last: Van Bortle

address: 3165 Porter Dr

department: Genetics

institute: Stanford University

description:
Biotin capture RNA-seq macrophage biological replicate 2.
Nascent RNA
Processed data file: PROseq_tDNA_counts.txt

data_processing:
Library strategy: PRO-seq
Biological replicates and experimental conditions (-PMA; +PMA) were sequenced together on an Illumina HiSeq2000 (paired-end, 100) for each individual experiment type (ATAC-seq, ChIP-seq, PRO-seq), and sequencing reads trimmed using trim galore v. 0.4.0, prior to downstream sequence alignment and analyses.
Trimmed ChIP and ATAC sequencing reads were mapped to the hg19 genome using Bowtie v 2.2.4, duplicate reads were removed by Picard tools v. 1.92 and mitochondrial reads filtered before peak-calling using MACS2 v. 2.1.0.
Alignment of sequencing reads to the current hg19 annotation of human tRNA genes (gtRNAdb; (Chan and Lowe 2009; Chan and Lowe 2016)) included the upstream and downstream 100 nt flanking genomic regions.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: tDNA count files were generated by extracting reads over tRNA genes (100nt flanking) and non-tRNA genes and normalized counts determined by DESeq.
Supplementary_files_format_and_content: *.txt: ATAC and ChIP peaks were determined using MACS2 v. 2.1.0. Changes in chromatin accessibility and histone occupancy were determined by differential read count analyses (EdgeR) over merged peak lists for each factor.

source_name: THP-1 cells, + PMA exposure

growth_protocol: THP-1 cells were obtained from ATCC (Lot # 62454382) and grown for multiple passages in T-75 flasks between 2-8 x 10^5 cells/mL in growth medium containing RPMI-1640 (Corning), 10% fetal bovine serum, and 1% penicillin streptomycin.

extract_protocol:
Equal numbers of THP-1 monocytes and THP-1 derived macrophages were collected (~5 million cells per PRO-seq experiment) and washed 3x in ice cold PBS, followed by resuspension and 5 minute incubation in 10 mL ice cold swelling buffer (10mM Tris-Cl pH 7.5, 2mM MgCl2, 3mM CaCl2). Cells were pelleted at 4C and resuspended in 1mL lysis buffer (swelling buffer + 0.5% Igepal, 10% glycerol, 2u/mL SUPERase In (Ambion)), and gently mixed 20x by pipetting with p1000 (pipette tip cutoff to reduce shearing). Nuclei were then pelleted (1,000 xg) and washed once with lysis buffer, pelleted (1,000 xg) and resuspended in 1mL nuclear storage buffer (50mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 100nM EDTA). Nuclei were again peletted and resuspended in 100 uL nuclear storage buffer. Nuclei were mixed with an equal volume of run-on reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20u SUPERase In (Ambion), 1% Sarkosyl, + 0.375mM biotin-11-A/C/G/UTP (Perkin-Elmer)), and incubated for 3 minutes at 30C. RNA was then extracted and isolated using the mirVana small RNA isolation kit (AM1560; Lot# 1412093). 1ug of purified small RNA was then incubated for 2 hrs at room temperature in 100 uL demethylation reaction buffer (600 mM KCl, 4mM MgCl2, 100uM NH4FeSO4, 600uM α-ketoglutarate, 4mM L-ascorbic acid, 100ug/mL bovine serum albumin (BSA), and 100 mM MES buffer (pH 5)) with 80 pmol ALKB, 160 pmol ALKB D135S. Expression and purification of tag-free ALKB (Lot# 716634S01) and ALKB D135S (Lot# 711466S04) was carried out by GenScript (Piscataway, NJ) and stored at ~0.2-0.5mg/mL in 50mM Tris-HCl, 150mM NaCl, 10% Glycerol, pH 8.0. Demethylation experiments were quenched in 10 mM EDTA, followed by pull-down of nascent biotinylated RNA via streptavidin magnetic beads (NEB #S1420S). Beads were washed in high salt buffer (2M NaCl, 50mM Tris-Cl pH 7.4, 0.5% Triton X-100), medium salt buffer (300mM NaCl, 10mM Tris-Cl pH 7.4, 0.1% Triton X-100), and low salt buffer (5mM Tris-Cl pH 7.4, 0.1% Triton X-100), and RNA library preparation subsequently carried out on beads, using the NEBnext small RNA library preparation kit (NEB #E7330S/L) with the minor modifications that RNA was denatured at 80C prior to adaptor ligation, and reverse transcription was carried out at increasing temperatures (50C for 1 hr, 60C for 30 minutes, 70C for 15 minutes). Following PCR amplification (12 cycles), DNA library was purified on a minElute column and subsequently size selected to remove primer dimer contamination.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For differentiation of THP-1 cells, non-adherent cells were diluted to 2 x 10^5 cells/mL and grown overnight, and a final concentration of 100 nM PMA was added the following morning. THP-1 derived macrophages were collected after 72 hr exposure to PMA by aspirating media and any non-adherent cells, and incubating adherent cells with TrypLE (ThermoFisher) for 15 minutes followed by cell wash in phosphate buffer saline (PBS) buffer.

tag: pma exposure

value: 72 hr PMA exposure

value: derived macrophages


title: CTCF_macrophage2

description:
ChIP-seq macrophage biological replicate 2.
Processed data file: CTCF_peak_edgeR_raw.txt

data_processing:
Biological replicates and experimental conditions (-PMA; +PMA) were sequenced together on an Illumina HiSeq2000 (paired-end, 100) for each individual experiment type (ATAC-seq, ChIP-seq, PRO-seq), and sequencing reads trimmed using trim galore v. 0.4.0, prior to downstream sequence alignment and analyses.
Trimmed ChIP and ATAC sequencing reads were mapped to the hg19 genome using Bowtie v 2.2.4, duplicate reads were removed by Picard tools v. 1.92 and mitochondrial reads filtered before peak-calling using MACS2 v. 2.1.0.
Alignment of sequencing reads to the current hg19 annotation of human tRNA genes (gtRNAdb; (Chan and Lowe 2009; Chan and Lowe 2016)) included the upstream and downstream 100 nt flanking genomic regions.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: tDNA count files were generated by extracting reads over tRNA genes (100nt flanking) and non-tRNA genes and normalized counts determined by DESeq.
Supplementary_files_format_and_content: *.txt: ATAC and ChIP peaks were determined using MACS2 v. 2.1.0. Changes in chromatin accessibility and histone occupancy were determined by differential read count analyses (EdgeR) over merged peak lists for each factor.

source_name: THP-1 cells, + PMA exposure, CTCF ChIP

extract_protocol:
Equal numbers of THP-1 monocytes and THP-1 derived macrophages were collected (~10 million cells per ChIP experiment) and resuspended in growth media at 1 x 10^6 cells/mL and cross-linked with rotation at room temperature in 1% formaldehyde for 10 minutes. Cross-linking was quenched with the addition of 200 mM glycine and an additional 5 minutes of rotation at room temperature. Cross-linked cells were then spun down and resuspended in 1x RIPA lysis buffer, followed by chromatin shearing via sonication (3 cycles using a Branson sonicator: 30 seconds on, 60 seconds off; 15 additional cycles on a Bioruptor sonicator: 30 seconds on, 30 seconds off). Individual ChIP experiments were performed on pre-cleared chromatin using antibody-coupled Dynabead protein G (ThermoFisher) magnetic beads. Anti-histone H3 (acetyl K27) antibody was obtained from Abcam (ab4729), POLR3D antibody was obtained from abcam (ab86786; Lot# GR267691-1), and anti-CTCF antibody was obtained from Millipore (07-729). 3-5 ug of antibody per ChIP was coupled to 18 uL beads and rotated overnight with sheared chromatin at 40 C. Beads were then washed 5x in ChIP wash buffer (Santa Cruz), 1x in TE, and chromatin eluted in TE + 1% SDS. Cross-linking was then reversed by incubation at 65C overnight, followed by digestion of RNA (30 min RNase incubation at 37C) and digestion of protein (30 min proteinase K incubation at 45C). ChIP DNA was then purified on a minElute column (Qiagen).
Libraries were prepared for sequencing using standard Illumina protocols.

value: anti-CTCF (Millipore 07-729)


title: CTCF_monocyte2

description:
ChIP-seq monocyte biological replicate 2.
Processed data file: CTCF_peak_edgeR_raw.txt

source_name: THP-1 cells, - PMA exposure, CTCF ChIP

value: ( - PMA )

value: monocytes


title: CTCF_macrophage1

description:
ChIP-seq macrophage biological replicate 1.
Processed data file: CTCF_peak_edgeR_raw.txt


title: B1-FD-#2-1600cells

description: Batch 1, mouse 1, food deprived


title: CTCF_monocyte1

description:
ChIP-seq monocyte biological replicate 1.
Processed data file: CTCF_peak_edgeR_raw.txt


title: shCUX1.810.rep2_RNA-seq

description:
processed data file:
EdgeRResults.txt

value: myeloid leukemia cell line


title: B3-Normal-#1-1200cells

description: Batch 3, mouse 1, normal


title: B1-FD-#1-300cells

description: Batch 1, mouse 1, food deprived


title: shCUX1.338.rep2_RNA-seq

description:
processed data file:
EdgeRResults.txt


title: PROseq_macrophage1

description:
Biotin capture RNA-seq macrophage biological replicate 1.
Nascent RNA
Processed data file: PROseq_tDNA_counts.txt


title: B0-normal2-#1-200cells

description: Batch 0, mouse 2, normal

value: Batch 0


title: PROseq_monocyte1

description:
Biotin capture RNA-seq monocyte biological replicate 1.
Nascent RNA
Processed data file: PROseq_tDNA_counts.txt

source_name: THP-1 cells, - PMA exposure


title: B0-normal1-#1-200cells

description: Batch 0, mouse 1, normal


title: B1-FD-#4-1200cells

description: Batch 1, mouse 1, food deprived


title: H3K27ac_monocyte2

description:
ChIP-seq monocyte biological replicate 2.
Processed data file: H3K27_peak_edgeR_raw.txt

source_name: THP-1 cells, - PMA exposure, H3K27ac ChIP

extract_protocol:
Equal numbers of THP-1 monocytes and THP-1 derived macrophages were collected (~10 million cells per ChIP experiment) and resuspended in growth media at 1 x 10^6 cells/mL and cross-linked with rotation at room temperature in 1% formaldehyde for 10 minutes. Cross-linking was quenched with the addition of 200 mM glycine and an additional 5 minutes of rotation at room temperature. Cross-linked cells were then spun down and resuspended in 1x RIPA lysis buffer, followed by chromatin shearing via sonication (3 cycles using a Branson sonicator: 30 seconds on, 60 seconds off; 15 additional cycles on a Bioruptor sonicator: 30 seconds on, 30 seconds off). Individual ChIP experiments were performed on pre-cleared chromatin using antibody-coupled Dynabead protein G (ThermoFisher) magnetic beads. Anti-histone H3 (acetyl K27) antibody was obtained from Abcam (ab4729), and POLR3D antibody was obtained from abcam (ab86786; Lot# GR267691-1). 3-5 ug of antibody per ChIP was coupled to 18 uL beads and rotated overnight with sheared chromatin at 40 C. Beads were then washed 5x in ChIP wash buffer (Santa Cruz), 1x in TE, and chromatin eluted in TE + 1% SDS. Cross-linking was then reversed by incubation at 65C overnight, followed by digestion of RNA (30 min RNase incubation at 37C) and digestion of protein (30 min proteinase K incubation at 45C). ChIP DNA was then purified on a minElute column (Qiagen).
Libraries were prepared for sequencing using standard Illumina protocols.

value: anti-H3K27ac (abcam ab4729)


title: H3K27ac_monocyte1

description:
ChIP-seq monocyte biological replicate 1.
Processed data file: H3K27_peak_edgeR_raw.txt


title: H3K27ac_macrophage2

description:
ChIP-seq macrophage biological replicate 2.
Processed data file: H3K27_peak_edgeR_raw.txt

source_name: THP-1 cells, + PMA exposure, H3K27ac ChIP


title: H3K27ac_macrophage1

description:
ChIP-seq macrophage biological replicate 1.
Processed data file: H3K27_peak_edgeR_raw.txt


title: Oocyte_3

description:
Chemical labeled genomic DNA
single cell

data_processing:
Library strategy: 5-formylcytosine-seq
Illumina CASAVA version 1.8 were used to the basecalling.
All sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads passed quality control were mapped to mouse reference genome (version: mm9) using bowtie.
Genome_build: mm9
Supplementary_files_format_and_content: The processed bed files include chromosome, start position, end position, reference genotype, regular CpG ("0") or 5fCpG ("1"), strand.

source_name: metaphase II oocyte

extract_protocol:
If started with the single cells, individual single cells were picked and seeded into the lysis buffer using the mouth pipette, and DNAs were released after proteinase treatment then malononnitrile labeled.If started from the bulk cells, genomic DNAs were first extracted from the cells using the Genomic DNA Clean and Concentrator kit (VisTech) based on the manufacturer’s instructions.
After malononnitrile treatment, single cell DNAs were amplified using MALBAC, and amplified DNAs were sonicated into 300-400 bp, and sequencing libraries were prepared under the instruction of NEBNext Ultra DNA Library Prep Kit for Illumina (NEB).

value: oocyte

tag: gender

value: female

tag: strain

tag: development stage

value: mature oocyte


title: Oocyte_6


title: Oocyte_8


title: Oocyte_11


title: shCUX1.810.rep1_RNA-seq

description:
processed data file:
EdgeRResults.txt


title: POLR3D_macrophage2

description:
ChIP-seq macrophage biological replicate 2.
Processed data file: POLR3D_tDNA_counts.txt

source_name: THP-1 cells, + PMA exposure, POLR3D ChIP

value: anti-POLR3D (abcam ab86786; lot# GR267691-1)


title: Oocyte_1


title: POLR3D_macrophage1

description:
ChIP-seq macrophage biological replicate 1.
Processed data file: POLR3D_tDNA_counts.txt


title: POLR3D_monocyte2

description:
ChIP-seq monocyte biological replicate 2.
Processed data file: POLR3D_tDNA_counts.txt

source_name: THP-1 cells, - PMA exposure, POLR3D ChIP


title: PROseq_monocyte2

description:
Biotin capture RNA-seq monocyte biological replicate 2.
Nascent RNA
Processed data file: PROseq_tDNA_counts.txt


title: Oocyte_10


title: POLR3D_monocyte1

description:
ChIP-seq monocyte biological replicate 1.
Processed data file: POLR3D_tDNA_counts.txt


title: ATAC-seq_macrophage2

description:
ATAC-seq macrophage biological replicate 2 sequencing replicate 4.
Processed data file: ATAC_peak_edgeR_raw.txt

extract_protocol:
Equal numbers of THP-1 monocytes and THP-1 derived macrophages were collected (50,000 cells per ATAC-seq experiment) and washed with 1x ice cold PBS. Cells were pelleted via centrifugation (500 xg, 5 minutes, 40C) and resuspended in cell lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), and immediately spun down (500 xg, 10 minutes, 40C). The supernatant was then discarded, and transposition reaction carried out for 30 minutes at 37C with Tn5 transposase in transposition buffer (Illumina, cat#FC-121-1030). DNA was immediately purified on a minElute column (Qiagen), followed by PCR amplification using the NEBNext high-fidelity master mix (NEB cat#M0541) with Nextera PCR primers and barcodes. PCR amplification was monitored as described (Buenrostro et al. 2015), and gel purified to remove contaminating primer-dimer species.
Libraries were prepared for sequencing using standard Illumina protocols.


title: Oocyte_5


title: ATAC-seq_macrophage1d

description:
ATAC-seq macrophage biological replicate 1 sequencing replicate 4.
Processed data file: ATAC_peak_edgeR_raw.txt


title: Oocyte_9


title: Oocyte_4


title: Oocyte_7


title: ATAC-seq_monocyte2d

description:
ATAC-seq monocyte biological replicate 2 sequencing replicate 4.
Processed data file: ATAC_peak_edgeR_raw.txt


title: ATAC-seq_macrophage2c

description:
ATAC-seq macrophage biological replicate 2 sequencing replicate 3.
Processed data file: ATAC_peak_edgeR_raw.txt


title: mESC_RR_2

description:
Chemical labeled genomic DNA
bulk

source_name: mouse embyronic stem cell

value: mouse ESC

value: male

value: inner cell mass


title: mESC_RR_1

description:
Chemical labeled genomic DNA
bulk


title: ATAC-seq_monocyte1d

description:
ATAC-seq monocyte biological replicate 1 sequencing replicate 4.
Processed data file: ATAC_peak_edgeR_raw.txt


title: ATAC-seq_macrophage1c

description:
ATAC-seq macrophage biological replicate 1 sequencing replicate 3.
Processed data file: ATAC_peak_edgeR_raw.txt


title: Oocyte_2


title: mESC_7


title: mESC_5


title: ATAC-seq_monocyte2c

description:
ATAC-seq monocyte biological replicate 2 sequencing replicate 3.
Processed data file: ATAC_peak_edgeR_raw.txt


title: mESC_2


title: ATAC-seq_macrophage1b

description:
ATAC-seq macrophage biological replicate 1 sequencing replicate 2.
Processed data file: ATAC_peak_edgeR_raw.txt


title: ATAC-seq_macrophage2b

description:
ATAC-seq macrophage biological replicate 2 sequencing replicate 2.
Processed data file: ATAC_peak_edgeR_raw.txt


title: mESC_4


title: mESC_6


title: ATAC-seq_monocyte1c

description:
ATAC-seq monocyte biological replicate 1 sequencing replicate 3.
Processed data file: ATAC_peak_edgeR_raw.txt


title: ATAC-seq_monocyte1b

description:
ATAC-seq monocyte biological replicate 1 sequencing replicate 2.
Processed data file: ATAC_peak_edgeR_raw.txt


title: adult_enterocytes_rep2_input (k27ac)

value: mixed C57BL/6 CD1

value: small intestine

tag: age

value: enterocyte


title: ATAC-seq_macrophage1a

description:
ATAC-seq macrophage biological replicate 1 sequencing replicate 1.
Processed data file: ATAC_peak_edgeR_raw.txt

value: 72 hr PMA exposure

value: derived macrophages


title: ATAC-seq_macrophage2a

description:
ATAC-seq macrophage biological replicate 2 sequencing replicate 1.
Processed data file: ATAC_peak_edgeR_raw.txt


title: ATAC-seq_monocyte2a

description:
ATAC-seq monocyte biological replicate 2 sequencing replicate 1.
Processed data file: ATAC_peak_edgeR_raw.txt

value: ( - PMA )


title: mESC_11

description:
Chemical labeled genomic DNA
single cell


title: ATAC-seq_monocyte1a

description:
ATAC-seq monocyte biological replicate 1 sequencing replicate 1.
Processed data file: ATAC_peak_edgeR_raw.txt

value: monocytes


title: mESC_12


title: mESC_8


title: mESC_3


title: ATAC-seq_monocyte2b

description:
ATAC-seq monocyte biological replicate 2 sequencing replicate 2.
Processed data file: ATAC_peak_edgeR_raw.txt


title: SAM24312815 Colon AKVPL derived tumor GFP- cells 1 GFP- AKVPL

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

source_name: RNA

extract_protocol: After FACS, cells were centrifuged at 1200rpm for 5 minutes. RNA was extracted from samples using the RNeasy Micro kit (cat # 74004; Qiagen) according to the manufacturer’s instructions and resuspended in a volume of 14ul. RNA quality was evaluated using Bioanalyzer.

tag: sample id

tag: primary tissue

value: Small Intestine

tag: inventory sample name

value: AKVPL derived tumor GFP- cells 1

value: GFP-

value: AKVPL


title: SAM24312806 Colon AKVPSL derived tumor GFP+ cells 2 GFP+ AKVPSL

value: AKVPSL derived tumor GFP+ cells 2

tag: sort

value: GFP+

tag: genotype

value: AKVPSL


title: SAM24312804 Colon AKVPSL derived tumor GFP+ cells 4 GFP+ AKVPSL

value: AKVPSL derived tumor GFP+ cells 4


title: RNAseq_RIL242_rep2

city: Cambridge

first: Mary

last: Gehring

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
PolyA RNA
Read length: 40

data_processing:
For all libraries: FastQC was used to examine read quality. Low-quality reads were removed with trim_galore with parameters --clip_R1 8, --clip_R2 8, --stringency 3, -q 25, -r1 32, -r2 32 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, version from 16 July 2014).
For all libraries: reads were initially aligned to a Col-Cvi “metagenome", created by substituting the Cvi allele of all SNPs into the TAIR10 assembly, then appending this pseudogenome to the TAIR10 (Col) sequence. Reads mapping ambiguously to the metagenome due to lack of SNPs in an area were then remapped to TAIR10. All reads were then filtered based on overlapping SNPs into reads definitively from Col, reads from Cvi, and all other reads. Bisulfite libraries were mapped using bismark v0.16.1 with parameters -N 1 and -L 40, and RNA-seq libraries were mapped using tophat v.2.0.13 with parameters -I 10000, -N 1 and --segment-length 20. All other parameters default.
Mapped bisulfite reads were further filtered to remove presumed PCR duplicates using a custom script provided with Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/), which removes duplicates randomly to minimize bias. Methylation information was then extracted using bismark_methylation_extractor. Resulting data were processed into BED-like format (see file description below) and saved with file format BSseq_{sample}_{context}.txt, where sample is the sample name (e.g. Col_1) and context is CpG, CHG or CHH (see below).
RIL genotypes were reconstructed using the depth of BS-seq reads overlapping SNPs. Coverage of reads overlapping SNPs was determined over 200bp windows for Col reads and Cvi reads separately, then smoothed using a moving average over 51 windows (centered) before calling putative genotype for each region.
htseq-count v0.6.1p1 was used to obtain total read counts for each gene from the mapped RNA-seq reads, with parameters -m union, with --stranded reverse. FPKM values were obtained using Cufflinks v2.2.1 (http://cole-trapnell-lab.github.io/cufflinks/), using a GTF file of the Araport11 A. thaliana annotations, --library-type fr-firststrand and all other parameters default.
Genome_build: Sequence used was A. thaliana TAIR10, annotations used were Araport 11 (https://www.araport.org/data/araport11),
Supplementary_files_format_and_content: BSseq_{sample}_{rep}_{context}.txt = per-cytosine methylation information for each sample (2 reps each) in each context (CpG, CHG and CHH), in BED-like format. First three fields indicate location of the cytosine (BED-like format, 0-based), fourth field is number of unmethylated reads at that position, fifth is number of methylated reads and sixth is % reads methylated. For CG data, data on the positive and negative strand have been combined into a single record by summing the methylated and unmethylated reads on each strand, and a seventh field indicates whether that CG contained data on only the forward strand (1), reverse strand (-1) or both (2).
Supplementary_files_format_and_content: RNAseq_{sample}_stats.txt contains RNA-seq data in tab-delimited format for each sample, with one row per gene. Contains gene ID (gene_id), gene coordinates (locus), FPKM (FPKM) and number of RNA-seq reads aligned to gene (raw_read_counts).
Supplementary_files_format_and_content: RIL{ril}_genotypes.bed contains consensus Col and Cvi regions in the indicated RIL (consensus = same in both replicates) in BED format, where the first three fields indicate a genomic region, and the fourth indicates whether that region is Col- or Cvi-genotype. Regions not covered in this BED file are undetermined - either inconsistent between replicates, unknown (e.g. around centromeres) or heterozygous.

organism: Arabidopsis thaliana

source_name: rosette leaves, Col/Cvi RIL242

growth_protocol: Plants were grown in a greenhouse with 16h light at 21C. Approx. 100mg leaf tissue was harvested from 3-wk-old rosettes.

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode GTCCGC.

treatment_protocol: No treatment.

tag: strain/background

value: Col/Cvi RIL242

tag: generation

value: 3 weeks

tag: tissue

value: rosette leaves


title: RNAseq_RIL242_rep3

description:
PolyA RNA
Read length: 40

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode GTGAAA.


title: SAM24312814 Colon AKVPL derived tumor GFP- cells 2 GFP- AKVPL

value: AKVPL derived tumor GFP- cells 2


title: SAM24312802 Colon AKVPSL derived tumor GFP- cells 2 GFP- AKVPSL

value: AKVPSL derived tumor GFP- cells 2


title: RNAseq_RIL124_rep3

description:
PolyA RNA
Read length: 40

source_name: rosette leaves, Col/Cvi RIL124

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode CCGTCC.

value: Col/Cvi RIL124


title: mESC_1

value: mouse ESC

value: male

value: inner cell mass


title: SAM24312813 Colon AKVPL derived tumor GFP- cells 3 GFP- AKVPL

value: Small Intestine

value: AKVPL derived tumor GFP- cells 3


title: RNAseq_RIL124_rep1

description:
PolyA RNA
Read length: 40

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode GCCAAT.


title: RNAseq_RIL124_rep2

description:
PolyA RNA
Read length: 40

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode ATGTCA.


title: SAM24312812 Colon AKVPL derived tumor GFP- cells 4 GFP- AKVPL

value: AKVPL derived tumor GFP- cells 4

value: GFP-


title: mESC_9


title: SAM24312816 Colon AKVPL derived tumor GFP+ cells 4 GFP+ AKVPL

value: AKVPL derived tumor GFP+ cells 4

value: AKVPL


title: RNAseq_cvi_rep3

description:
PolyA RNA
Read length: 40

source_name: rosette leaves, Cvi-0 parent line

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode AGTTCC.

value: Cvi-0 parent line


title: mESC_10


title: RNAseq_cvi_rep2

description:
PolyA RNA
Read length: 40

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode AGTCAA.


title: RNAseq_cvi_rep1

description:
PolyA RNA
Read length: 40

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode ACAGTG.


title: SAM24312818 Colon AKVPL derived tumor GFP+ cells 2 GFP+ AKVPL

value: AKVPL derived tumor GFP+ cells 2

value: GFP+


title: SAM24312805 Colon AKVPSL derived tumor GFP+ cells 3 GFP+ AKVPSL

value: AKVPSL derived tumor GFP+ cells 3

value: AKVPSL


title: RNAseq_col_rep2

description:
PolyA RNA
Read length: 40

source_name: rosette leaves, Col-0 parent line

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode CGATGT.

value: Col-0 parent line

value: 3 weeks

value: rosette leaves


title: RNAseq_col_rep3

description:
PolyA RNA
Read length: 40

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode CTTGTA.


title: SAM24312819 Colon AKVPL derived tumor GFP+ cells 1 GFP+ AKVPL

value: AKVPL derived tumor GFP+ cells 1


title: SAM24312801 Colon AKVPSL derived tumor GFP- cells 3 GFP- AKVPSL

value: AKVPSL derived tumor GFP- cells 3


title: RNAseq_col_rep1

description:
PolyA RNA
Read length: 40

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode TGACCA.


title: SAM24312807 Colon AKVPSL derived tumor GFP+ cells 1 GFP+ AKVPSL

value: AKVPSL derived tumor GFP+ cells 1


title: RNAseq_RIL242_rep1

description:
PolyA RNA
Read length: 40

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol.
Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode CAGATC.

value: Col/Cvi RIL242


title: SAM24312817 Colon AKVPL derived tumor GFP+ cells 3 GFP+

value: Small Intestine

value: AKVPL derived tumor GFP+ cells 3


title: SAM24312800 Colon AKVPSL derived tumor GFP- cells 4 GFP- AKVPSL

value: AKVPSL derived tumor GFP- cells 4

value: GFP-


title: SAM24312803 Colon AKVPSL derived tumor GFP- cells 1 GFP- AKVPSL

value: Colon

value: AKVPSL derived tumor GFP- cells 1


title: BM_Eng_3

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: Ensembl genebuild 76 (mouse assembly GRCm38).
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

source_name: Phagocytic macrophage

growth_protocol: Paired subpopulations of phagocytic (engulfing, Eng) and non-phagocytic (non-engulfing, Non) mouse macrophages, were sorted by FACS from three different tissues (Spleen, Bone Marrow and Intestine). Three replicate sample pairs (Eng, Non) were prepared from each tissue, resulting in a total of 18 samples.

extract_protocol:
Samples were amplified with the Ovation Single Cell kit (NuGen). The amount of starting material was 2 ng.
cDNA was prepared using the standard Ilumina TrueSeq RNAseq library preparation kit. Libraries were prepared in two batches.

value: Bone marrow

tag: phenotype

value: Engulfing

tag: library batch

tag: sample pair


title: Int_Non_2

value: Intestine

value: Non engulfing


title: Int_Non_1


title: Int_Non_4


title: Int_Eng_1


title: BM_Eng_4


title: Int_Eng_2


title: Int_Eng_4


title: Spl_Eng_2

value: Spleen


title: Spl_Eng_1


title: BM_Non_3


title: BM_Eng_1


title: BM_Non_4


title: BM_Non_1


title: Spl_Eng_4


title: Spl_Non_4


title: Spl_Non_2


title: Spl_Non_1


title: pymt-12wk-RNAseq-rep3

city: bronx

first: ying

last: cai

state: New York

address: 1300 morris park ave

institute: Albert Einstein College of Medicine

description: Sample 23

data_processing:
The reads were aligned to the mouse genome(mm9) with GSNAP
The raw gene counts by Htseq
Genome_build: mm9
Supplementary_files_format_and_content: raw gene counts in txt file

source_name: pymt-late-caricnoma-tumor

extract_protocol:
Mammary tissue was snap-froze, later total RNA was extracted with miRNeasy (Qiagen).
Libraries were prepared according to Illumina's instructions.

value: mammary gland


title: pymt-10wk-RNAseq-rep3

description: Sample 21

source_name: pymt-early-carcinoma-tumor


title: pymt-8wk-RNAseq-rep3

description: Sample 19

source_name: pymt-adenoma/MIN-tumor


title: fvb-12wk-RNAseq-rep3

description: Sample 24

source_name: fvb-mammary-gland


title: pymt-6wk-RNAseq-rep3

description: Sample 17

source_name: pymt-hyperplasia-mammary-gland


title: fvb-6wk-RNAseq-rep3

description: Sample 18


title: fvb-8wk-RNAseq-rep3

description: Sample 20


title: BSseq_Col_rep1

description:
Bisulfite-treated genomic DNA
Read length: 40x40, 100x100, 50x50

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol with index ATCACG sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50).

value: Col-0 parent line

value: 3 weeks

value: rosette leaves


title: fvb-12wk-RNAseq-rep2

description: Sample 16


title: fvb-10wk-RNAseq-rep2

description: Sample 14


title: pymt-8wk-RNAseq-rep2

description: Sample 11


title: pymt-12wk-RNAseq-rep2

description: Sample 15


title: pymt-10wk-RNAseq-rep2

description: Sample 13


title: pymt-6wk-RNAseq-rep2

description: Sample 9


title: fvb-6wk-RNAseq-rep2

description: Sample 10


title: pymt-6wk-RNAseq-rep1

description: Sample 1


title: pymt-8wk-RNAseq-rep1

description: Sample 3


title: fvb-8wk-RNAseq-rep2

description: Sample 12


title: WT Female 3 RNAseq

status: Public on Mar 28 2017

city: New York

first: Joseph

middle: M

last: Luna

state: NY

address: 1230 York Ave #64

institute: The Rockefeller University

data_processing:
Alignment: Fastq files were processed with kallisto on an index built from Ensembl release 85 mm10 trancripts;  kallisto -b 100 --single -l 100 -s 25; pachterlab.github.io/kallisto/
Expression testing: kallisto output was processed with sleuth for expression testing between WT and KO samples; http://pachterlab.github.io/sleuth/
Transcript with highest mean expression across all sample was selected as representative per gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes sleuth output, gene symbol, and pseudocount matrix per sample

source_name: Liver

extract_protocol:
RNA was extracted from tissue using Trizol
RNAseq libraries were prepared for sequencing using standard Illumina protocols with Poly-A selection

treatment_protocol: Flash frozen mouse livers were pulverzied in liquid nitrogen. Two-thirds of powder was UV crosslinked at 254nM for CLIP. Remaining third was left uncrosslinked for RNAseq.

tag: mir122 status

value: WT

tag: Sex

value: Female

tag: mouse id

tag: sample type

value: RNAseq


title: WT Male 5 RNAseq

value: Male


title: WT Female 2 RNAseq


title: fvb-12wk-RNAseq-rep1

description: Sample 8


title: WT Female 1 RNAseq


title: pymt-10wk-RNAseq-rep1

description: Sample 5


title: fvb-10wk-RNAseq-rep1

description: Sample 6


title: fvb-8wk-RNAseq-rep1

description: Sample 4


title: WT Male 4 RNAseq


title: KO Male 3 CLIP

data_processing:
quality filtering: minimum quality filter applied for barcode and insert; fastq_filter.pl; -if sanger -f min:0-3:20,mean:20-40:20 -maxN -1 -v -of fasta ;github.com/chaolinzhanglab/ctk/tree/v1.0.3
collapse exact sequences: exact duplicate sequences removed; fasta2collapse.pl; ;github.com/chaolinzhanglab/ctk/tree/v1.0.3
trim 5' adapter sequence: 5' 20 nucleotides trimmed (NNNNAGGGAGGACGATGCGG, where NNNN is 4 nucleotide index for multiplexing); fastx Trimmer; -f 21; http://hannonlab.cshl.edu/fastx_toolkit/
strip 5' degenerate linker: 5 nucleotide (NNNNG) degenerate barcode stripped and appended to read IDs; stripBarcode.pl; -linker 5 ; github.com/chaolinzhanglab/ctk/tree/v1.0.3
remove 3' adapter sequene: 3' adapter GTGTCAGTCACTTCCAGCGG clipped; fastx Clipper; -l 20 -a GTGTCAGTCACTTCCAGCGG -n; http://hannonlab.cshl.edu/fastx_toolkit/
Groomed reads aligned to mm10 with bowtie2 using defaults
Collapse PCR duplicates: mapped reads with same 5' end and same degenerate barcode consolidated; tag2collapse.pl; keep-tag-name --keep-max-score --random-linker -EM 30 --seq-error-model em-local --weight --weight-in-name ; github.com/chaolinzhanglab/ctk/tree/v1.0.3
Collapsed mapped reads were clustered, where the peak cluster coordinate +/- 32 nt was searched for the presence of miRNA 6-8mers, for those miRNAs with CLIP evidence.
Fold changes were calculated by adding a psuedocount of 1 to every cluster, normalizing each cluster for read depth (reads per million mapped), and dividing by condition.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes CLIP-seq cluster definition and locations, miRNA seed search results, and genomic annotations

extract_protocol:
UV crosslinked cells were lysed in 1x PXL buffer, lysates were Dnase treated, partially RnaseI digested, clarified by centrifugation, and Argonaute-mRNA complexes isolated with pan-Ago 2A8 antibody.
CLIP libraries were prepared as in Luna, JM et al (2015). 1st PCR Products were amplified in a second round of PCR that added a 4 nt index (for multiplexing) and a 16 nt common primer sequence. Raw files are demultiplexed on the basis of this index, but have not been further modified.
CLIPseq

value: KO

value: CLIP


title: fvb-10wk-RNAseq-rep3

description: Sample 22


title: KO Female 1 CLIP


title: KO Female 1 RNAseq


title: KO Male 2 RNAseq


title: KO Male 4 CLIP


title: KO Male 3 RNAseq


title: KO Male 2 CLIP


title: pymt-12wk-RNAseq-rep1

description: Sample 7


title: fvb-6wk-RNAseq-rep1

description: Sample 2


title: WT Male 4 CLIP


title: WT Female 1 CLIP


title: WT Female 2 CLIP


title: WT Female 3 CLIP