title: yFR912_W0012_kin28as-bur2D_Rpb3_Rep2_06-07-11

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

hyb_protocol: Hybridization: Add 110uL of hybridization buffer (100uL DIGEasy Buffer, 5uL 10mg/mL Salmon Sperm DNA, 5uL 8mg/mL yeast tRNA) to the resuspended (mixed) colored pellet. Put at 95C for 5 minutes, centrifuge briefly and transfer at 42C for 10 min (Keep samples at 42C while waiting for hybridization). Follow standard Agilent chamber hybridization protocols. Incubate overnight (16-24h) at 42C in Agilent hybridization oven at 20 rpm rotation speed.    Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.  Ref: Bataille A.R., Robert F. Methods in Enzymology 2009.    Stripping: Stripping is done in 1L of 5 mM Potassium phosphate buffer pH 6.6 after scanning of the slides. 1) Use a crystallization dish, and a metallic slide rack (use weighing spatulas to lift the rack from the bottom of the dish and avoid direct contact with the hot surface). Submerge the rack with slides (from 1 to 10) in stripping buffer and heat it up slowly on heating plate until the liquid boils with big bubbles. It usually takes 15 to 20 minutes. Do not overboil it. 2) Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations.

scan_protocol: Scanner Axon GenePix4000B and GenePix Pro (version 6.1.0.4) extraction software were used for scanning and features quantification. Scan at 100% laser power for both channels. Set the Pixel Size to 5um / pixel. Set the Lines to average to 1. Set the Focus Position to 0uM. Set the minimal intensity (histogram preview) to 3000-5000. Adjust PMTs so that approximately 5-10% spots are saturated. This is done to ensure full dynamic range utilization. Adjust PMTs so that the intensity ratio is 0.9 - 1.1 (when possible).

data_processing: The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)) and replicates were combined using a weighted average method as described previously (Pokholok et al., 2005).

organism: Saccharomyces cerevisiae

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL mQH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 400ng of DNA diluted to 40uL with mQH2O. Incubate 20 minutes at 12C. Add 12uL of a the following mix: 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly. Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -20'C for at least 30 min, then spin 20 minutes at 4C. Wash the pellet with 700uL -20'C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL mQH2O and place on ice.    Ligation: Thaw everything on ice, and do all manipulations on ice (or in cold room). Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL mQH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C. Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20'C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (visible as a smear on the side of the tube) with 700uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL mQH2O.    Labeling: Add 15uL of PCR aa-dUTP mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL mQH2O) to resuspended ligation samples. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL mQH2O)(Pause program if necessary). PCR cycling conditions: 1) 5:00 at 55C 2) 5:00 at 72C 3) 2:00 at 95C 4) 0:30 at 95C 5) 0:30 at 55C 6) 1:00 at 72C 7) Repeat steps 4-6 31 more times. 8) 4:00 at 72C 9) Forever at 4C. Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also elute twice with 40uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO (Use DMSO store in vacuum with desiccant). Resuspended dyes are store in the dark at -80?C. Mix well, and incubate at room temperature in the dark for one hour. Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, elute twice in 40uL.  Speed-vac until ~10uL is left, or to dryness (corresponding Cy3 and Cy5 samples can be mixed before speed-vac in order to avoid DNA loss upon later resuspension).  Ref: Bataille A.R., Robert F. Methods in Enzymology 2009.

growth_protocol: Culture were done at 30C in YEP+2% Glucose media (50 to 200mL) inoculated at OD600 0.1 from an overnight preculture in the appropriate media. Culture were allowed to grow until it reach OD600 0.6-0.8 before the ATP analog NAPP1 was added at 6uM final concentration and the cells left to grow an additional 15min at 30C. Cultures were poured in 50mL Falcon tubes containing 1.4mL 37% formaldehyde for crosslinking (1% final), and incubate on rotating wheel for 30 min at room temperature. Crosslinking was stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde (~125mM final). Crosslinked cells were pelleted at 4 C, 3000 rpm ( in Beckman centrifuge (GS 6R Rotor 3.8)), resuspended in 40mL ice cold TBS and pelleted again. This wash was repeated a second time. Cell pellets were resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells were pelleted by centrifugation, the supernatant removed by pipetting, and the cells snap-freeze in liquid nitrogen. Cells were store at -80 C. Ref: Bataille A.R., Robert F. Methods in Enzymology 2009

extract_protocol: Cells are thawed on ice, and resuspended in 700mL lysis buffer with protease inhibitors (50mM HEPES-KOH, pH 7.5; 140mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% Na-deoxycholate; 1mM PMSF; 1mM Benzamidine; 10ug/mL Aprotinin; 1ug/mL Leupeptin; 1ug/mL Pepstatin). 500uL of acid-washed glass beads (Sigma) are added, and the cells lysed using the bead-beater (4x5min cycles, with 5min breaks on ice). The tubes are pierced with a 18-gauge syringe needle and place in 2mL collection tubes to allow transfer of lysate, but not beads, with a brief centrifugation. The lysates are then homogenized by pipetting and sonicated 4x 20sec at output 7 Watts, with a 1 minute break between sonication cycles. The sonicated lysates are centrifuge for 5 min at 4 C max speed and supernatant used immediately for ChIP (or snap-freeze in liquid nitrogen and saved frozen at -80C).    For immunoprecipitation, Dynabeads (details at the end of the section) (50uL / ChIP) are washed twice with PBS + 0.5% BSA (freshly made), and resuspended in PBS + 0.5% BSA. Antibody are added (Concentration and souce at the end of the section), and incubated overnight at 4 C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL (PBS/BSA or Lysis buffer) / ChIP. 30uL of resuspended beads/antibody are added to 400-600uL of lysate, and incubated overnight at 4 C in haematological mixer. Beads are then washed in cold room (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors)(50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate ), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl, twice with ice cold Wash Buffer (10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA), and once with ice cold TE. Remaining liquid is removed by pipetting after 1 min centrifugation at 4 C (max speed). 50uL TE + 1% SDS is added and beads are incubated overnight at 65 C for elution and reverse crosslink. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65C to reverse the crosslinks with the ChIP samples.  For this study the anti-myc (9E10) was a kind gift from Alain Verreault. The anti-Flag (M2) was from Sigma. The 3E8, 3E10 and 4E12 antibodies were purchased from Helmholtz Zentrum in Munich. The H5 (P-Ser2) and H14 (P-Ser5) were purchased from Covance. The anti-Rpb3 (W0012) was purchased from Neoclone Biotechnology. The 8WG16 (Ab817) antibody was purchased from Abcam.The following amounts of antibody per immunoprecipitation were used: 3E8 (5μL), 3E10 (5μL), 4E12 (5μL), 8WG16 (2μg), H14 (15μg), H5 (15μg), W0012 (3μL), 9E10 (5μg), M2 (5μg). The antibodies were coupled to Dynabeads (Invitrogen) coated with protein G (3E8, 3E10, 4E12), IgG Pan mouse antibodies (8WG16, H14, W0012, 9E10, M2) or Sheep anti-mouse IgG (H5).    To clean up the DNA, beads are spun down and supernatant is transfered to a new 1.5mL tube. 350uL of a solution of 345uL TE / 3uL RNAse A (10mg/mL) / 2uL Glycogen (20mg/mL) is added to the supernatant and samples incubated at 37C for 2 hours. 15uL of 10% SDS and 7.5uL Proteinase K are then added and the tubes incubated for another 2 hours at 37 C. The samples are then extracted twice with 400uL phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated with 14uL of 5M NaCl (for about 350uL of extracted sample) and 1mL of freezing 100% EtOH (-20 C). Pellets are washed with 700uL 70% EtOH (-20 C) and left to air dry for few minutes before they are resuspended in 50uL TE. Stored ChIP samples at -20 C.  Ref: Bataille A.R., Robert F. Methods in Enzymology 2009.

tag: strain

tag: antibody

tag: vendor

value: Neoclone Biotechnology


title: LeftAtrium_IschemicCardiomyopathy_Male_3

status: Public on Feb 01 2012

type: RNA

city: St. Louis

first: Christina

middle: Marie

last: Ambrosi

state: MO

address: 1 Brookings Drive

department: Biomedical Engineering

country: USA

institute: Washington University in St. Louis

description: ISCHEMIC MALE LA 3

data_processing: A relative quantification method (Livak and Schmittgen, 2001) based on the cycle at threshold (Ct) value was employed with GAPDH as an endogenous control and Nonfailing Male LV 2 as the calibrator sample.

label: Taqman

molecule: total RNA

organism: Homo sapiens

source_name: left atrium, ischemic cardiomyopathy

label_protocol: Total RNA (1-2 μg) was first converted to cDNA using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).  Subsequent reactions were performed using 100 ng of cDNA loaded into each well of our custom-designed gene arrays mixed with Taqman Universal PCR Master Mix (Applied Biosystems).

extract_protocol: Total RNA was extracted from a total of 68 samples using the RNEasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.  RNA yield was measured using a Nanodrop 1000 (Thermo Scientific) and quality was assessed by verifying the presence of 18S and 28S bands as run on a 1% agarose gel.

treatment_protocol: Cardiac tissue preparations were preserved in RNAlater (Sigma-Aldrich, St. Louis, MO) and stored at -80 degrees Celsius until RNA extraction.

tag: tissue type

value: Left atrium

tag: gender

value: Male

tag: age

tag: disease state

value: Ischemic cardiomyopathy


title: 12727.s1

type: genomic

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

scan_protocol: Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan

data_processing: Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).

label: biotin nucleotide or dinitrophenyl labeled

molecule: genomic DNA

source_name: leukocyte

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: cell type

value: leukocyte

tag: sample id

tag: sentrix id

tag: sentrix position

value: C

tag: experiment

tag: group

tag: family

tag: distribution

tag: site

value: xm

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: white


title: yFR912_H5_kin28as-bur2D_Ser2_Rep2_06-07-11

tag: strain

tag: antibody

value: H5 (Ser2)

tag: vendor

value: Covance


title: yFR763_H5_kin28as_Ser2_Rep2_06-07-11


title: yFR912_H5_kin28as-bur2D_Ser2_Rep1_06-07-11


title: yFR763_W0012_kin28as_Rpb3_Rep2_06-07-11


title: yFR912_W0012_kin28as-bur2D_Rpb3_Rep1_06-07-11


title: 12720.s1

hyb_protocol: Followed the manufacturer's (Illumina) specifications

tag: gender

value: E

value: xx


title: yFR763_H5_kin28as_Ser2_Rep1_06-07-11


title: 12741.s1

value: G


title: 12770.s1

value: D

value: fl


title: 12688.s1

value: A

value: hv


title: 12701.s1

value: more-than-one-race


title: 12705.s1

value: F


title: 12695.s1

value: Male

value: B

value: native-hawaiian


title: HG_CTL51

source_name: lymphoblast

value: lymphoblast


title: LeftAtrium_IschemicCardiomyopathy_Male_1

description: ISCHEMIC MALE LA 1

tag: tissue type

value: Left atrium

tag: age

tag: disease state

value: Ischemic cardiomyopathy


title: LeftAtrium_IschemicCardiomyopathy_Male_2

description: ISCHEMIC MALE LA 2


title: HG_CTL52

tag: cell type

tag: sample id

tag: sentrix id

value: H


title: 12683.s1

value: leukocyte

tag: sentrix position

value: I

tag: experiment

tag: group

value: oi

value: white


title: 12669.s1

tag: family

tag: distribution

tag: site

value: vn


title: LeftVentricle_IschemicCardiomyopathy_Female_4

description: ISCHEMIC FEMALE LV 4

source_name: left ventricle, ischemic cardiomyopathy

value: Left ventricle

value: Female


title: 12679.s1

value: E

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: yFR763_W0012_kin28as_Rpb3_Rep1_06-07-11

tag: strain

tag: antibody

tag: vendor

value: Neoclone Biotechnology


title: yFR762_H5_WTkin28as_Ser2_Rep2_06-07-11

value: H5 (Ser2)

value: Covance


title: yFR762_W0012_WTkin28as_Rpb3_Rep2_06-07-11


title: LeftVentricle_IschemicCardiomyopathy_Female_3

description: ISCHEMIC FEMALE LV 3

tag: tissue type

tag: gender

tag: age


title: LeftVentricle_IschemicCardiomyopathy_Female_2

description: ISCHEMIC FEMALE LV 2

tag: disease state


title: 12673.s1

tag: cell type

tag: sample id

value: Male

tag: sentrix id

value: hv


title: 12682.s1

tag: sentrix position

value: B

tag: experiment

tag: group

value: pb


title: LeftVentricle_IschemicCardiomyopathy_Female_1

description: ISCHEMIC FEMALE LV 1

value: Ischemic cardiomyopathy


title: 12642.s1

tag: family

tag: distribution

tag: site

value: kr


title: HG_CTL50

value: lymphoblast

value: F


title: 11993.s1.2

value: leukocyte

value: L

value: xm

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: 12690.s1

value: C

value: vn

value: white


title: yFR762_W0012_WTkin28as_Rpb3_Rep1_06-07-11

tag: strain

tag: antibody

tag: vendor

value: Neoclone Biotechnology


title: yFR762_H5_WTkin28as_Ser2_Rep1_06-07-11

value: H5 (Ser2)


title: 12680.s1

tag: gender

value: A


title: LeftAtrium_IschemicCardiomyopathy_Female_2

description: ISCHEMIC FEMALE LA 2

tag: tissue type

value: Left atrium

value: Female

tag: age

tag: disease state


title: LeftAtrium_IschemicCardiomyopathy_Female_3

description: ISCHEMIC FEMALE LA 3


title: yFR682_W0012_bur2D_Rpb3_Rep2_06-07-11

growth_protocol: Culture were done at 30C in YEP+2% Glucose media (50 to 200mL) inoculated at OD600 0.1 from an overnight preculture in YEP+2% Glucose media. Culture were allowed to grow until it reach OD600 0.6-1.0, poured in 50mL Falcon tubes containing 1.4mL 37% formaldehyde for crosslinking (1% final), and incubate on rotating wheel for 30 min at room temperature. Crosslinking was stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde (~125mM final). Crosslinked cells were pelleted at 4 C, 3000 rpm ( in Beckman centrifuge (GS 6R Rotor 3.8)), resuspended in 40mL ice cold TBS and pelleted again. This wash was repeated a second time. Cell pellets were resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells were pelleted by centrifugation, the supernatant removed by pipetting, and the cells snap-freeze in liquid nitrogen. Cells were store at -80 C. Ref: Bataille A.R., Robert F. Methods in Enzymology 2009


title: yFR682_H5_bur2D_Ser2_Rep2_06-07-11

value: Covance


title: LeftAtrium_IschemicCardiomyopathy_Female_4

description: ISCHEMIC FEMALE LA 4


title: LeftAtrium_IschemicCardiomyopathy_Female_1

description: ISCHEMIC FEMALE LA 1


title: 12646.s1

tag: cell type

tag: sample id

value: Male

tag: sentrix id

value: D


title: 12656.s1

tag: sentrix position

tag: experiment

tag: group

value: kc


title: 12623.s1

value: I

tag: family

tag: distribution

tag: site

value: xx


title: 12619.s1

value: leukocyte

value: J

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: yFR682_H5_bur2D_Ser2_Rep1_06-07-11

tag: strain

tag: antibody

tag: vendor


title: yFR551_H5_ctk1D_Ser2_Rep2_06-07-11


title: yFR682_W0012_bur2D_Rpb3_Rep1_06-07-11


title: yFR551_W0012_ctk1D_Rpb3_Rep1_06-07-11


title: yFR551_W0012_ctk1D_Rpb3_Rep2_06-07-11


title: yFR117_W0012_S288C_Rpb3_Rep2_06-07-11


title: 12647.s1

tag: gender

value: E


title: 12603.s1


title: 12616.s1


title: HG_CTL49

value: lymphoblast


title: 12621.s1

value: L


title: yFR117_H5_S288C_Ser2_Rep2_06-07-11


title: yFR551_H5_ctk1D_Ser2_Rep1_06-07-11


title: 12588.s1

value: hv

value: white


title: 12499.s1

value: fl


title: 12595.s1

value: G

value: more-than-one-race


title: HG_CTL48

value: F


title: 12563.s1


title: 12517.s1

value: ox


title: 12541.s1

value: Male

value: B

value: vn


title: 12501.s1

value: H


title: 12492.s1

value: sb


title: HG_CTL47


title: 12510.s1

value: leukocyte


title: 12478.s1

value: J

value: african-amer


title: L226_647 environment 2

city: Ithaca

first: Jesse

middle: D.

last: Munkvold

state: NY

address: 240 Emerson

department: Plant Breeding and Genetics

institute: Cornell University

description: array batch 20202

hyb_protocol: Prehybridization and hybridization was done using the Pronto! Hybridization Kit (Corning) with accompanying protocols. Labeled A555 and A647 samples were combined in balanced dye ratios and hybridization was done in Corning Microarray Hybridization chammber II with Erie Scientific Raised Coverslips (25x60mm). Hybridization was carried out for 18hrs. in a 42C water bath.

scan_protocol: Scanning was done using an Axon 6000B scanner with automatic PMT gain, 100% laser power, and 10um resolution.

data_processing: Array, block, and spot detection was done automatically and inspected by hand. Bad spots were automatically and hand-flagged.Background was calculated by morphological opening followed by closing using the GenePix 6 software.

label: Alexa 555

organism: Triticum aestivum

source_name: Pre-anthesis spike bulk

label_protocol: 10ug of total RNA were amplified using the amino allyly MessageAmp II aRNA Amplification kit (Ambion). Alexa 555 or 647 (Invitrogen #A32755) dyes were coupled according to accompanying protocols. Dye incorporation was measured using photospectrometry.

growth_protocol: Plants were grown in the  field (Ketola 2005) near Ithaca, NY. Spike samples were harvested at physiological maturity as described in Munkvold et al. 2009. TAG. 119. Samples were stored at -20C for two months while embryo samples were harvested. Primary and secondary position seeds were selected from five spikes and embryos (~100) were isolated by hand, frozen in liquid nitrogen, and stored at -80C.

extract_protocol: Total RNA extraction from isolated embryos was done using the Trizol reagent with only slight modifications to the manufacturer protocol. Total RNA was treated with RQ1 DNAse and cleaned using Qiagen Rneasy columns.

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

label: Alexa 647

source_name: CxC Line 226, embryo at physiological maturity

value: embryo at physiological maturity


title: yFR117_W0012_S288C_Rpb3_Rep1_06-07-11

value: Neoclone Biotechnology


title: yFR117_H5_S288C_Ser2_Rep1_06-07-11

value: H5 (Ser2)

value: Covance


title: 12481.s1

tag: cell type

tag: sample id

tag: sentrix id

tag: sentrix position

value: A

value: oi

value: native-american


title: HG_CTL46

value: lymphoblast

value: Male

value: D

tag: experiment

tag: group


title: L221_647 environment 2

description: array batch 20556

source_name: CxC Line 221, embryo at physiological maturity


title: 12483.s1

value: C

tag: family

tag: distribution

tag: site

value: ox

tag: cpea dx

value: white


title: 12451.s1

value: leukocyte

value: I

value: pb

tag: age at collection (months)

tag: ethnicity


title: 12445.s1

tag: gender

value: kr


title: 12449.s1

value: J


title: 12438.s1


title: 12457.s1

value: B

value: lu


title: 12618.s1

value: xx


title: HG_CTL45


title: 12394.s1

value: K


title: L213_647 environment 2

description: array batch 20202

tag: population

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

value: Pre-anthesis spike bulk

source_name: CxC Line 213, embryo at physiological maturity

value: embryo at physiological maturity


title: 12412.s1

value: Male

value: E

value: hv


title: L215_647 environment 2

description: array batch 20574

tag: field location

source_name: CxC Line 215, embryo at physiological maturity


title: L214_647 environment 2

description: array batch 20202

tag: year

source_name: CxC Line 214, embryo at physiological maturity


title: 12437.s1

value: D

value: vn

value: white


title: yFR778_H5_SSU72wt_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR778 (Wt for yFR552 degron-ssu72 ) cells, after 1 H at 37 C

growth_protocol: Culture were done at 30C in YEP+2% Glucose media (50 to 200mL) inoculated at OD600 0.1 from an overnight preculture in YEP+2% Glucose media. Culture were allowed to grow until it reach OD600 0.5-0.8 and transfered to 37C for 1H before crosslinking. Culture were poured in 50mL Falcon tubes containing 1.4mL 37% formaldehyde for crosslinking (1% final), and incubate on rotating wheel for 30 min at room temperature. Crosslinking was stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde (~125mM final). Crosslinked cells were pelleted at 4 C, 3000 rpm ( in Beckman centrifuge (GS 6R Rotor 3.8)), resuspended in 40mL ice cold TBS and pelleted again. This wash was repeated a second time. Cell pellets were resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells were pelleted by centrifugation, the supernatant removed by pipetting, and the cells snap-freeze in liquid nitrogen. Cells were store at -80 C. Ref: Bataille A.R., Robert F. Methods in Enzymology 2009

tag: strain

tag: antibody

value: H5 (Ser2)

tag: vendor

value: Covance


title: 12432.s1

tag: cell type

value: leukocyte

tag: sample id

tag: sentrix id

value: G

value: asian


title: yFR778_4E12_SSU72wt_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR778 (Wt for yFR552 degron-ssu72 ) cells, after 1 H at 37 C

value: Helmholtz Zentrum


title: 12390.s1

tag: sentrix position

value: I

tag: experiment

tag: group


title: yFR778_8WG16_SSU72wt_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR778 (Wt for yFR552 degron-ssu72 ) cells, after 1 H at 37 C

value: 8WG16 (CTD)

value: Abcam


title: L212_647 environment 2

description: array batch 20202

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 212, embryo at physiological maturity


title: yFR778_H5_SSU72wt_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR778 (Wt for yFR552 degron-ssu72 ) cells, after 1 H at 37 C


title: HG_CTL44

value: lymphoblast

value: Male

value: B


title: L209_647 environment 2

description: array batch 20574

source_name: CxC Line 209, embryo at physiological maturity

value: embryo at physiological maturity


title: L208_647 environment 2

description: array batch 20202

source_name: CxC Line 208, embryo at physiological maturity


title: yFR778_4E12_SSU72wt_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR778 (Wt for yFR552 degron-ssu72 ) cells, after 1 H at 37 C


title: 12361.s1

value: K

tag: family

tag: distribution

tag: site

value: xx

tag: cpea dx

value: white


title: 12346.s1

value: leukocyte

tag: gender

value: C

value: kc

tag: age at collection (months)

tag: ethnicity


title: L206_647 environment 2

description: array batch 20574

tag: population

tag: field location

tag: year

source_name: CxC Line 206, embryo at physiological maturity


title: 12382.s1

tag: cell type

value: L

value: pb


title: L205_647 environment 2

description: array batch 20202

source_name: CxC Line 205, embryo at physiological maturity


title: 12314.s1

tag: sample id


title: L210_647 environment 2

description: array batch 20556

source_name: CxC Line 210, embryo at physiological maturity


title: yFR778_3E8_SSU72wt_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR778 (Wt for yFR552 degron-ssu72 ) cells, after 1 H at 37 C

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: 12383.s1

tag: sentrix id

tag: sentrix position

value: D

tag: experiment

tag: group

value: xm


title: L201_647 environment 2

description: array batch 20202

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

tag: tissue

source_name: CxC Line 201, embryo at physiological maturity


title: 12329.s1

value: I

tag: family

tag: distribution

tag: site

value: sb

tag: cpea dx


title: HG_CTL42

value: lymphoblast

tag: gender

value: Male

value: J


title: L207_647 environment 2

description: array batch 20574

tag: population

tag: field location

value: Pre-anthesis spike bulk

source_name: CxC Line 207, embryo at physiological maturity

value: embryo at physiological maturity


title: yFR778_3E8_SSU72wt_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR778 (Wt for yFR552 degron-ssu72 ) cells, after 1 H at 37 C


title: 12296.s1

source_name: leukocyte

tag: cell type

value: leukocyte

value: K

value: oi

tag: age at collection (months)

tag: ethnicity

value: white


title: 12304.s1

tag: sample id

value: E


title: L197_647 environment 2

description: array batch 20202

tag: year

source_name: CxC Line 197, embryo at physiological maturity


title: yFR778_3E10_SSU72wt_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR778 (Wt for yFR552 degron-ssu72 ) cells, after 1 H at 37 C

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: 12289.s1

tag: sentrix id

tag: sentrix position

tag: experiment

tag: group

value: vn


title: 12337.s1

value: F

tag: family

tag: distribution

tag: site

value: hv

value: more-than-one-race


title: HG_CTL41

source_name: lymphoblast

tag: gender

value: I


title: 12316.s1

value: D

value: fl

tag: cpea dx


title: HG_CTL43

tag: cell type

value: lymphoblast

value: Male

value: A


title: yFR552_H5_degron-Ssu72_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR552 degron-ssu72 cells, after 1 H at 37 C

value: H5 (Ser2)

value: Covance


title: yFR778_8WG16_SSU72wt_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR778 (Wt for yFR552 degron-ssu72 ) cells, after 1 H at 37 C

value: 8WG16 (CTD)

value: Abcam


title: L198_647 environment 2

description: array batch 20574

source_name: Pre-anthesis spike bulk

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 198, embryo at physiological maturity

value: embryo at physiological maturity


title: 12257.s1

value: leukocyte

tag: sample id

value: F

value: xm

tag: age at collection (months)

tag: ethnicity

value: white


title: L200_647 environment 2

description: array batch 20556

tag: year

source_name: CxC Line 200, embryo at physiological maturity


title: L196_647 environment 2

description: array batch 20202

source_name: CxC Line 196, embryo at physiological maturity


title: 12297.s1

tag: sentrix id

value: oi


title: yFR778_3E10_SSU72wt_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR778 (Wt for yFR552 degron-ssu72 ) cells, after 1 H at 37 C

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: 12275.s1

tag: sentrix position

tag: experiment

tag: group

tag: family

value: vn


title: 12418.s1

tag: gender

value: Male

tag: distribution

tag: site

value: sb

tag: cpea dx


title: 12252.s1

tag: cell type

value: G

value: kr

value: other


title: L195_647 environment 2

description: array batch 20202

tag: population

tag: field location

tag: tissue

source_name: CxC Line 195, embryo at physiological maturity


title: yFR552_4E12_degron-Ssu72_P-Ser7_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR552 degron-ssu72 cells, after 1 H at 37 C


title: HG_CTL40

value: lymphoblast

tag: sample id

value: H


title: yFR552_8WG16_degron-Ssu72_CTD_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR552 degron-ssu72 cells, after 1 H at 37 C

value: 8WG16 (CTD)

value: Abcam


title: L191_647 environment 2

description: array batch 20556

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

tag: year

value: Pre-anthesis spike bulk

source_name: CxC Line 191, embryo at physiological maturity

value: embryo at physiological maturity


title: 12225.s1

value: leukocyte

tag: sentrix id

value: L

value: pb

tag: age at collection (months)

tag: ethnicity

value: white


title: L189_647 environment 2

description: array batch 20202

source_name: CxC Line 189, embryo at physiological maturity


title: L194_647 environment 2

description: array batch 20574

source_name: CxC Line 194, embryo at physiological maturity


title: 12243.s1

value: Male

tag: sentrix position

value: D

value: ox


title: yFR552_8WG16_degron-Ssu72_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR552 degron-ssu72 cells, after 1 H at 37 C

tag: strain

tag: antibody

tag: vendor


title: yFR552_3E8_degron-Ssu72_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR552 degron-ssu72 cells, after 1 H at 37 C

value: Helmholtz Zentrum


title: 12230.s1

tag: gender

value: J

tag: experiment

tag: group

tag: family

value: sb


title: 12255.s1

tag: cell type

value: C

tag: distribution

tag: site

value: kr

tag: cpea dx


title: 12239.s1

tag: sample id

value: A


title: yFR552_4E12_degron-Ssu72_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR552 degron-ssu72 cells, after 1 H at 37 C


title: yFR552_H5_degron-Ssu72_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR552 degron-ssu72 cells, after 1 H at 37 C

value: H5 (Ser2)

value: Covance


title: HG_CTL39

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

value: lymphoblast

value: G


title: L176_647 environment 2

description: array batch 20202

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 176, embryo at physiological maturity

value: embryo at physiological maturity


title: yFR552_3E8_degron-Ssu72_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR552 degron-ssu72 cells, after 1 H at 37 C


title: yFR552_3E10_degron-Ssu72_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR552 degron-ssu72 cells, after 1 H at 37 C


title: L175_647 environment 2

description: array batch 20574

source_name: CxC Line 175, embryo at physiological maturity


title: 12235.s1

value: leukocyte

value: Male

tag: sentrix id

tag: sentrix position

value: B

tag: age at collection (months)

tag: ethnicity

value: white


title: 12224.s1

tag: gender


title: 12201.s1

value: J

tag: experiment

value: ox

value: other


title: 12206.s1

value: K

tag: group

value: sb


title: 12157.s1

value: I

tag: family


title: 12227.s1

tag: cell type

value: E

value: pb


title: yFR552_3E10_degron-Ssu72_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR552 degron-ssu72 cells, after 1 H at 37 C

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: L168_647 environment 2

description: array batch 20202

value: Cayuga x Caledonia, DH

source_name: CxC Line 168, embryo at physiological maturity


title: 12173.s1

tag: sample id

value: H

tag: distribution

tag: site

value: hv

tag: cpea dx


title: L167_647 environment 2

description: array batch 20202

tag: population

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 167, embryo at physiological maturity

value: embryo at physiological maturity


title: L166_647 environment 2

description: array batch 20556

source_name: CxC Line 166, embryo at physiological maturity


title: 12070.s1

value: leukocyte

value: Male

tag: sentrix id

tag: sentrix position

value: lu

tag: age at collection (months)

tag: ethnicity


title: L169_647 environment 2

description: array batch 20202

source_name: CxC Line 169, embryo at physiological maturity


title: yFR912_8WG16_Kin28as_bur2D_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR912 kinb28-as bur2D cells, after 15min with 6uM NAPP1

value: 8WG16 (CTD)

value: Abcam


title: yFR912_4E12_Kin28as_bur2D_P-Ser7_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR912 kinb28-as bur2D cells, after 15min with 6uM NAPP1


title: HG_CTL37

value: lymphoblast

tag: gender

tag: experiment

tag: group


title: 12152.s1

source_name: leukocyte

tag: cell type

tag: family

value: kr

value: white


title: 12202.s1

tag: sample id

value: B

value: oi

value: more-than-one-race


title: yFR912_4E12_Kin28as_bur2D_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR912 kinb28-as bur2D cells, after 15min with 6uM NAPP1

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: yFR912_8WG16_Kin28as_bur2D_CTD_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR912 kinb28-as bur2D cells, after 15min with 6uM NAPP1


title: yFR912_3E8_Kin28as_bur2D_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR912 kinb28-as bur2D cells, after 15min with 6uM NAPP1


title: L158_647 environment 2

description: array batch 20574

tag: population

value: Cayuga x Caledonia, DH

source_name: CxC Line 158, embryo at physiological maturity


title: HG_CTL38

source_name: lymphoblast

value: F


title: L153_647 environment 2

description: array batch 20574

source_name: Pre-anthesis spike bulk

tag: field location

value: Ketola, Cornell University, Ithaca, NY

source_name: CxC Line 153, embryo at physiological maturity


title: 12099.s1

tag: distribution

tag: site

tag: cpea dx


title: yFR912_3E8_Kin28as_bur2D_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR912 kinb28-as bur2D cells, after 15min with 6uM NAPP1


title: L162_647 environment 2

description: array batch 20556

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 162, embryo at physiological maturity


title: 12056.s1

tag: sentrix id

tag: sentrix position

tag: age at collection (months)

tag: ethnicity


title: L146_647 environment 2

description: array batch 20202

source_name: CxC Line 146, embryo at physiological maturity

value: embryo at physiological maturity


title: L147_647 environment 2

description: array batch 20556

source_name: CxC Line 147, embryo at physiological maturity


title: 12033.s1

tag: cell type

value: leukocyte

tag: gender

value: H

tag: experiment

tag: group

value: kc

value: asian


title: 12051.s1

tag: sample id

value: Male

value: E

tag: family

value: gv


title: 12096.s1

value: C

value: xm

value: white


title: 12041.s1

value: K

value: lu

value: african-amer


title: yFR912_3E10_Kin28as_bur2D_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR912 kinb28-as bur2D cells, after 15min with 6uM NAPP1

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: HG_CTL36

value: lymphoblast

value: D


title: L143_647 environment 2

description: array batch 20556

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

value: Pre-anthesis spike bulk

source_name: CxC Line 143, embryo at physiological maturity

value: embryo at physiological maturity


title: HG_CTL34


title: HG_CTL35


title: 12037.s1

value: leukocyte

value: B

tag: distribution

tag: site

value: pb

tag: cpea dx


title: yFR912_3E10_Kin28as_bur2D_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR912 kinb28-as bur2D cells, after 15min with 6uM NAPP1


title: yFR763_8WG16_kin28as_CTD_NAPP1_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR763 kin28-as cells, after 15min with 6uM NAPP1

value: 8WG16 (CTD)

value: Abcam


title: 12020.s1

value: Male

tag: sentrix id

tag: sentrix position

value: J

value: oi


title: 11969.s1

value: xm

tag: age at collection (months)

tag: ethnicity

value: white


title: yFR763_8WG16_kin28as_CTD_NAPP1_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR763 kin28-as cells, after 15min with 6uM NAPP1


title: 12068.s1

tag: cell type

tag: gender

value: xx


title: 12044.s1

value: F

tag: experiment

tag: group

value: vn


title: 11966.s1

tag: sample id

value: L

tag: family

value: ox


title: L130_647 environment 2

description: array batch 20556

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 130, embryo at physiological maturity


title: L132_647 environment 2

description: array batch 20556

tag: population

source_name: CxC Line 132, embryo at physiological maturity

value: embryo at physiological maturity


title: 11933.s1

value: leukocyte

value: H

value: pb


title: yFR763_4E12_kin28as_P-Ser7_NAPP1_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR763 kin28-as cells, after 15min with 6uM NAPP1

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: 11949.s1

value: Male

value: B

tag: distribution

tag: site

value: lu

tag: cpea dx


title: yFR763_3E8_kin28as_P-Ser5_NAPP1_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR763 kin28-as cells, after 15min with 6uM NAPP1


title: HG_CTL33

value: lymphoblast

tag: sentrix id

tag: sentrix position

value: A


title: 11990.s1

tag: cell type

value: I

tag: age at collection (months)

tag: ethnicity

value: asian


title: L128_647 environment 2

description: array batch 20556

tag: field location

source_name: CxC Line 128, embryo at physiological maturity


title: yFR763_3E8_kin28as_P-Ser5_NAPP1_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR763 kin28-as cells, after 15min with 6uM NAPP1


title: 11957.s1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

tag: sample id

tag: gender

value: G

tag: experiment

tag: group


title: 11947.s1

value: F

tag: family

value: xm

value: white


title: 11935.s1

value: C

value: fl


title: HG_CTL32

value: L


title: L129_647 environment 2

description: array batch 20202

tag: population

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 129, embryo at physiological maturity

value: embryo at physiological maturity


title: L135_647 environment 2

description: array batch 20202

source_name: CxC Line 135, embryo at physiological maturity


title: 11939.s1

value: leukocyte

value: Male

value: D

tag: distribution

value: kc

value: more-than-one-race


title: yFR763_4E12_kin28as_P-Ser7_NAPP1_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR763 kin28-as cells, after 15min with 6uM NAPP1

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: L124_647 environment 2

description: array batch 20202

source_name: CxC Line 124, embryo at physiological maturity


title: yFR763_3E10_kin28as_P-Ser2_NAPP1_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR763 kin28-as cells, after 15min with 6uM NAPP1


title: L125_647 environment 2

description: array batch 20202

source_name: CxC Line 125, embryo at physiological maturity


title: L138_647 environment 2

description: array batch 20556

source_name: CxC Line 138, embryo at physiological maturity


title: HG_CTL31

value: lymphoblast

tag: sentrix id

tag: sentrix position

value: K


title: 11909.s1

source_name: leukocyte

tag: cell type

value: G

tag: site

value: sb

tag: cpea dx

tag: age at collection (months)


title: yFR762_4E12_KIN28wt_P-Ser7_NAPP1_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR762 (wt for yFR763 kin28as) cells, after 15min with 6uM NAPP1


title: yFR762_4E12_KIN28wt_P-Ser7_NAPP1_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR762 (wt for yFR763 kin28as) cells, after 15min with 6uM NAPP1


title: 11922.s1

tag: sample id

tag: gender

value: H

tag: ethnicity

value: white


title: 11942.s1

value: E

tag: experiment

tag: group

tag: family

value: kr


title: yFR762_8WG16_KIN28wt_CTD_NAPP1_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR762 (wt for yFR763 kin28as) cells, after 15min with 6uM NAPP1

value: 8WG16 (CTD)

value: Abcam


title: 11946.s1

value: A

value: ox


title: yFR763_3E10_kin28as_P-Ser2_NAPP1_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR763 kin28-as cells, after 15min with 6uM NAPP1


title: L116_647 environment 2

description: array batch 20556

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 116, embryo at physiological maturity

value: embryo at physiological maturity


title: L115_647 environment 2

description: array batch 20202

source_name: CxC Line 115, embryo at physiological maturity


title: 11835.s1

value: leukocyte

value: Male

tag: distribution

value: fl


title: 11888.s1

tag: sentrix id


title: 11897.s1

tag: sentrix position

value: xm


title: L117_647 environment 2

description: array batch 20556

source_name: Pre-anthesis spike bulk

source_name: CxC Line 117, embryo at physiological maturity


title: L118_647 environment 2

description: array batch 20556

source_name: CxC Line 118, embryo at physiological maturity


title: 11895.s1

tag: cell type

value: F

value: hv


title: 11860.s1

value: L

tag: site

value: white


title: yFR762_8WG16_KIN28wt_CTD_NAPP1_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR762 (wt for yFR763 kin28as) cells, after 15min with 6uM NAPP1

tag: strain

tag: antibody

tag: vendor


title: L119_647 environment 2

description: array batch 20556

source_name: CxC Line 119, embryo at physiological maturity


title: 11894.s1

tag: sample id

tag: gender

value: B

tag: cpea dx

tag: age at collection (months)

value: more-than-one-race


title: 11834.s1

tag: experiment

tag: group

tag: family

tag: ethnicity


title: yFR762_3E8_KIN28wt_P-Ser5_NAPP1_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR762 (wt for yFR763 kin28as) cells, after 15min with 6uM NAPP1

value: Helmholtz Zentrum


title: 11824.s1

value: G


title: 11800.s1

value: J

value: sb


title: yFR762_3E10_KIN28wt_P-Ser2_NAPP1_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR762 (wt for yFR763 kin28as) cells, after 15min with 6uM NAPP1


title: HG_CTL29

source_name: lymphoblast

value: lymphoblast

value: I


title: L114_647 environment 2

description: array batch 20202

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 114, embryo at physiological maturity

value: embryo at physiological maturity


title: yFR762_3E8_KIN28wt_P-Ser5_NAPP1_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR762 (wt for yFR763 kin28as) cells, after 15min with 6uM NAPP1


title: L112_647 environment 2

description: array batch 20202

source_name: CxC Line 112, embryo at physiological maturity


title: 11740.s1

tag: cell type

value: leukocyte

value: Male

tag: sentrix id

tag: sentrix position

tag: distribution

value: kr


title: HG_CTL30


title: L111_647 environment 2

description: array batch 20202

source_name: CxC Line 111, embryo at physiological maturity


title: 11788.s1

value: H

tag: site

value: kc


title: 11773.s1

tag: sample id

value: A

value: oi

value: white


title: 11792.s1

tag: gender

value: B

value: ox


title: HG_CTL28


title: yFR999_8WG16_srb10D_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR999 srb10D cells

tag: strain

tag: antibody

value: 8WG16 (CTD)

tag: vendor

value: Abcam


title: yFR999_4E12_srb10D_P-Ser7_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR999 srb10D cells

value: Helmholtz Zentrum


title: 11711.s1

value: I

tag: experiment

tag: group

value: fl

tag: cpea dx

tag: age at collection (months)


title: yFR999_3E8_srb10D_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR999 srb10D cells


title: yFR999_4E12_srb10D_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR999 srb10D cells


title: L107_647 environment 2

description: array batch 20574

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

value: Pre-anthesis spike bulk

source_name: CxC Line 107, embryo at physiological maturity


title: 11722.s1

value: leukocyte

value: Male

value: K

tag: family

value: vn

tag: ethnicity


title: 11721.s1

tag: cell type

tag: sentrix id

value: E

value: kc


title: L106_647 environment 2

description: array batch 20202

tag: year

tag: tissue

source_name: CxC Line 106, embryo at physiological maturity

value: embryo at physiological maturity


title: L104_647 environment 2

description: array batch 20202

source_name: CxC Line 104, embryo at physiological maturity


title: 11714.s1

tag: sample id

tag: sentrix position

value: B

tag: distribution

tag: site

value: kr

value: white


title: yFR999_3E8_srb10D_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR999 srb10D cells

tag: strain

tag: antibody

tag: vendor


title: 11716.s1

tag: gender

value: C

tag: experiment

tag: group

tag: cpea dx


title: yFR999_8WG16_srb10D_CTD_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR999 srb10D cells

value: 8WG16 (CTD)

value: Abcam


title: 11691.s1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

value: A

tag: family

tag: age at collection (months)


title: L102_647 environment 2

description: array batch 20574

tag: population

value: Cayuga x Caledonia, DH

tag: field location

source_name: CxC Line 102, embryo at physiological maturity


title: L98_647 environment 2

description: array batch 20556

value: Ketola, Cornell University, Ithaca, NY

tag: year

source_name: CxC Line 98, embryo at physiological maturity


title: 11666.s1

tag: cell type

tag: sentrix id

value: fl

tag: ethnicity


title: 11679.s1

value: leukocyte

tag: sample id

tag: sentrix position

value: L

tag: distribution

value: hv


title: yFR999_3E10_srb10D_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR999 srb10D cells

tag: strain

tag: antibody

value: Helmholtz Zentrum


title: 11673.s1

tag: gender

value: Male

tag: site


title: L96_647 environment 2

description: array batch 20202

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 96, embryo at physiological maturity


title: yFR999_3E10_srb10D_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR999 srb10D cells

tag: vendor


title: 11685.s1

source_name: leukocyte

value: E

tag: experiment

tag: group

tag: family

tag: cpea dx


title: yFR958_8WG16_ess1H164R_CTD_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR958 ess1-H164R cells


title: HG_CTL27

value: lymphoblast

value: G


title: L95_647 environment 2

description: array batch 20202

tag: population

tag: field location

tag: year

source_name: CxC Line 95, embryo at physiological maturity

value: embryo at physiological maturity


title: yFR958_8WG16_ess1H164R_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR958 ess1-H164R cells


title: yFR958_4E12_ess1H164R_P-Ser7_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR958 ess1-H164R cells


title: HG_CTL26

tag: cell type

tag: sentrix id

value: F


title: 11665.s1

tag: sample id

tag: sentrix position

value: vn

tag: age at collection (months)

tag: ethnicity

value: white


title: 11491.s1

tag: gender

value: K

tag: distribution


title: yFR958_3E8_ess1H164R_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR958 ess1-H164R cells

tag: strain

tag: antibody


title: 11628.s1

tag: experiment

tag: site

value: xx


title: 11634.s1

value: H

tag: group

tag: family

value: kc

value: other


title: 11630.s1

value: leukocyte

tag: cpea dx

value: not-specified


title: L93_647 environment 2

description: array batch 20202

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: tissue

source_name: CxC Line 93, embryo at physiological maturity


title: L92_647 environment 2

description: array batch 20556

source_name: Pre-anthesis spike bulk

tag: year

value: Pre-anthesis spike bulk

source_name: CxC Line 92, embryo at physiological maturity


title: 11610.s1

tag: cell type

tag: sample id

value: Male

tag: sentrix id

value: J

value: xm


title: yFR958_4E12_ess1H164R_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR958 ess1-H164R cells

tag: vendor

value: Helmholtz Zentrum


title: 11653.s1

tag: gender

tag: sentrix position

value: I

tag: age at collection (months)

tag: ethnicity


title: 11638.s1

value: B

tag: experiment

tag: distribution

value: oi


title: L88_647 environment 2

description: array batch 20556

source_name: CxC Line 88, embryo at physiological maturity

value: embryo at physiological maturity


title: L90_647 environment 2

description: array batch 20574

source_name: CxC Line 90, embryo at physiological maturity


title: HG_CTL25

source_name: lymphoblast

value: lymphoblast

value: E

tag: group


title: yFR958_3E8_ess1H164R_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR958 ess1-H164R cells

tag: strain

tag: antibody


title: 11470.s3

tag: family

tag: site

value: hv

tag: cpea dx

value: white


title: L87_647 environment 2

description: array batch 20574

tag: population

tag: field location

tag: year

tag: tissue

source_name: CxC Line 87, embryo at physiological maturity


title: L86_647 environment 2

description: array batch 20202

source_name: CxC Line 86, embryo at physiological maturity


title: 11407.s1

tag: cell type

value: leukocyte

tag: sample id

tag: sentrix id

value: L

value: pb


title: yFR958_3E10_ess1H164R_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR958 ess1-H164R cells

tag: vendor


title: yFR958_3E10_ess1H164R_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR958 ess1-H164R cells


title: 11616.s1

tag: gender

tag: sentrix position

value: C

value: vn

tag: age at collection (months)

tag: ethnicity


title: 11431.s1

value: Male

value: G

tag: experiment

tag: group

tag: distribution


title: 11372.s1

tag: family

tag: site

value: kc


title: L85_647 environment 2

description: array batch 20556

tag: population

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

value: Pre-anthesis spike bulk

source_name: CxC Line 85, embryo at physiological maturity


title: L80_647 environment 2

description: array batch 20574

tag: field location

source_name: CxC Line 80, embryo at physiological maturity


title: yFR957_8WG16_ESS1wt_CTD_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR957 (Wt for yFR958 ess1-H164R)  cells

tag: strain

tag: antibody

value: 8WG16 (CTD)

value: Abcam


title: 11241.s1

tag: cell type

value: K

tag: cpea dx


title: yFR957_8WG16_ESS1wt_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR957 (Wt for yFR958 ess1-H164R)  cells


title: 11456.s1

tag: sample id

tag: sentrix id

value: E


title: 11393.s1

tag: gender

value: hv


title: HG_CTL24

value: lymphoblast

tag: sentrix position

value: D


title: L81_647 environment 2

description: array batch 20574

tag: year

tag: tissue

source_name: CxC Line 81, embryo at physiological maturity

value: embryo at physiological maturity


title: 11347.s1

value: leukocyte

value: H

tag: experiment

value: kr

tag: age at collection (months)

tag: ethnicity

value: white


title: yFR957_3E8_ESS1wt_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR957 (Wt for yFR958 ess1-H164R)  cells

tag: vendor

value: Helmholtz Zentrum


title: yFR957_4E12_ESS1wt_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR957 (Wt for yFR958 ess1-H164R)  cells


title: 11232.s1

value: Male

tag: group

tag: family

tag: distribution

tag: site

value: pb


title: yFR957_4E12_ESS1wt_P-Ser7_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR957 (Wt for yFR958 ess1-H164R)  cells

tag: strain

tag: antibody


title: 11262.s1

tag: cell type

value: I

value: ox

tag: cpea dx


title: HG_CTL23

tag: sample id

tag: sentrix id

value: C


title: 11229.s1

tag: gender

tag: sentrix position

value: B

value: fl


title: 11132.s1

value: K


title: 11110.s1

value: L

value: vn

value: asian


title: L73_647 environment 2

description: array batch 20202

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 73, embryo at physiological maturity

value: embryo at physiological maturity


title: L69_647 environment 2

description: array batch 20202

source_name: CxC Line 69, embryo at physiological maturity


title: L75_647 environment 2

description: array batch 20574

source_name: CxC Line 75, embryo at physiological maturity


title: L79_647 environment 2

description: array batch 20574

source_name: CxC Line 79, embryo at physiological maturity


title: 11177.s1

source_name: leukocyte

value: leukocyte

tag: experiment

value: hv

tag: age at collection (months)

tag: ethnicity

value: white


title: yFR957_3E8_ESS1wt_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR957 (Wt for yFR958 ess1-H164R)  cells

tag: vendor

value: Helmholtz Zentrum


title: HG_CTL22

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

value: lymphoblast

value: Male

tag: group


title: 11106.s1

value: D

tag: family

tag: distribution

tag: site


title: 11158.s1

tag: cell type

value: F

value: pb

tag: cpea dx

value: african-amer


title: yFR957_3E10_ESS1wt_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR957 (Wt for yFR958 ess1-H164R)  cells

tag: strain

tag: antibody


title: 11074.s1

tag: sample id

tag: gender

tag: sentrix id

tag: sentrix position

value: K

value: kr


title: 11066.s1

value: I


title: yFR957_3E10_ESS1wt_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR957 (Wt for yFR958 ess1-H164R)  cells


title: L68_647 environment 2

description: array batch 20202

tag: population

value: Cayuga x Caledonia, DH

tag: field location

tag: year

tag: tissue

source_name: CxC Line 68, embryo at physiological maturity


title: L65_647 environment 2

description: array batch 20202

value: Ketola, Cornell University, Ithaca, NY

source_name: CxC Line 65, embryo at physiological maturity


title: yFR945_9E10_pti1-3xmyc_Rep2

description: Biological replicate 2 of 2. Pti1 occupancy (Pti1-3myc), using 9E10 antibody, measured by the IP Tag/Ip NoTag ratio,  yFR945 pti1-3myc/yFR116 Wt cells

tag: source

value: Alain Verreault

value: Myc 9E10


title: yFR945_9E10_pti1-3xmyc_Rep1

description: Biological replicate 1 of 2. Pti1 occupancy (Pti1-3myc), using 9E10 antibody, measured by the IP Tag/Ip NoTag ratio,  yFR945 pti1-3myc/yFR116 Wt cells


title: 11010.s1

value: leukocyte

tag: experiment

tag: group

value: fl

tag: age at collection (months)

tag: ethnicity


title: L66_647 environment 2

description: array batch 20556

source_name: Pre-anthesis spike bulk

value: Pre-anthesis spike bulk

source_name: CxC Line 66, embryo at physiological maturity

value: embryo at physiological maturity


title: HG_CTL20

tag: cell type

value: lymphoblast


title: 11090.s1

value: Male

value: E

tag: family

tag: distribution

tag: site

value: vn

tag: cpea dx

value: white


title: 11027.s1

tag: sample id

tag: gender

value: H


title: L56_647 environment 2

description: array batch 20202

source_name: CxC Line 56, embryo at physiological maturity


title: yFR943_9E10_3xmyc-ssu72_Rep1

description: Biological replicate 1 of 2. Ssu72 occupancy (3myc-Ssu72), using 9E10 antibody, measured by the IP Tag/Ip NoTag ratio,  yFR943 3myc-ssu72/yFR116 Wt cells

tag: strain

tag: antibody


title: HG_CTL21

tag: sentrix id

tag: sentrix position

value: A


title: 11350.s1

value: F

value: kc

value: more-than-one-race


title: 11458.s1

value: L

value: xm


title: yFR787_H5_CTD-S7A_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells

value: H5 (Ser2)

tag: vendor

value: Covance


title: 11498.s1

value: leukocyte

value: B

value: sb


title: yFR943_9E10_3xmyc-ssu72_Rep2

description: Biological replicate 2 of 2. Ssu72 occupancy (3myc-Ssu72), using 9E10 antibody, measured by the IP Tag/Ip NoTag ratio,  yFR943 3myc-ssu72/yFR116 Wt cells

tag: source

value: Alain Verreault

value: Myc 9E10


title: L64_647 environment 2

description: array batch 20556

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 64, embryo at physiological maturity

value: embryo at physiological maturity


title: L59_647 environment 2

description: array batch 20556

source_name: CxC Line 59, embryo at physiological maturity


title: yFR787_W0012_CTD-S7A_Rpb3_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using W0012 (anti-Rpb3) antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells

value: Neoclone Biotechnology


title: L63_647 environment 2

description: array batch 20202

source_name: CxC Line 63, embryo at physiological maturity


title: HG_CTL18

source_name: lymphoblast

tag: cell type

value: lymphoblast

value: Male

value: G

tag: experiment

tag: group


title: yFR787_W0012_CTD-S7A_Rpb3_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using W0012 (anti-Rpb3) antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells


title: L54_647 environment 2

description: array batch 20202

source_name: CxC Line 54, embryo at physiological maturity


title: 11406.s1

tag: family

tag: distribution

tag: site

value: kr

tag: age at collection (months)

tag: ethnicity

value: more-than-one-race


title: HG_CTL19

tag: sample id

tag: gender

value: I


title: 11495.s1

tag: sentrix id

tag: sentrix position

value: A

value: pb

tag: cpea dx

value: white


title: L48_647 environment 2

description: array batch 20556

tag: population

source_name: CxC Line 48, embryo at physiological maturity


title: 11524.s1

value: leukocyte

value: K

value: xm


title: 11581.s1

value: E


title: L51_647 environment 2

description: array batch 20556

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

source_name: CxC Line 51, embryo at physiological maturity


title: L50_647 environment 2

description: array batch 20556

tag: year

value: Pre-anthesis spike bulk

source_name: CxC Line 50, embryo at physiological maturity

value: embryo at physiological maturity


title: yFR787_H5_CTD-S7A_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells

tag: strain

tag: antibody

value: H5 (Ser2)

tag: vendor

value: Covance


title: L47_647 environment 2

description: array batch 20574

tag: tissue

source_name: CxC Line 47, embryo at physiological maturity


title: 11578.s1

tag: cell type

value: Male

tag: experiment

tag: group

tag: family


title: yFR787_H14_CTD-S7A_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using H14 antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells


title: HG_CTL17

value: lymphoblast


title: 11499.s1

tag: distribution

tag: site

value: fl

tag: age at collection (months)

tag: ethnicity


title: 11483.s1

tag: sample id

tag: gender

tag: sentrix id

tag: sentrix position

value: J

value: kc

value: more-than-one-race


title: HG_CTL16

value: C


title: L46_647 environment 2

description: array batch 20556

tag: population

tag: field location

tag: year

source_name: CxC Line 46, embryo at physiological maturity


title: 11413.s1

value: leukocyte

value: G

value: xx

tag: cpea dx

value: white


title: yFR787_H14_CTD-S7A_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using H14antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells

tag: strain

tag: antibody

tag: vendor


title: 11489.s1

tag: cell type

value: B

tag: experiment

tag: group

value: xm


title: L45_647 environment 2

description: array batch 20574

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 45, embryo at physiological maturity


title: yFR787_4E12_CTD-S7A_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells

value: Helmholtz Zentrum


title: yFR787_4E12_CTD-S7A_P-Ser7_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells


title: 11565.s1

source_name: leukocyte

value: Male

value: F

tag: family

tag: distribution

tag: site

tag: age at collection (months)


title: yFR787_3E8_CTD-S7A_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells


title: L44_647 environment 2

description: array batch 20202

source_name: CxC Line 44, embryo at physiological maturity

value: embryo at physiological maturity


title: HG_CTL4

value: lymphoblast

tag: sample id

tag: gender

tag: sentrix id

value: I


title: yFR787_3E10_CTD-S7A_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells


title: yFR787_3E8_CTD-S7A_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells


title: L36_647 environment 2

description: array batch 20556

tag: population

tag: field location

source_name: CxC Line 36, embryo at physiological maturity


title: L32_647 environment 2

description: array batch 20556

source_name: Pre-anthesis spike bulk

tag: year

source_name: CxC Line 32, embryo at physiological maturity


title: 11349.s1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

tag: sentrix position

value: D

value: kr

tag: cpea dx

tag: ethnicity

value: asian


title: 11168.s1

tag: cell type

value: leukocyte

value: G

value: hv


title: 11124.s1

value: B

tag: experiment

value: white


title: HG_CTL15

value: A

tag: group


title: 11146.s1

value: K

value: pb


title: L34_647 environment 2

description: array batch 20202

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 34, embryo at physiological maturity


title: 11063.s1

value: Male

tag: family


title: 11014.s1

tag: distribution

value: fl


title: L37_647 environment 2

description: array batch 20202

source_name: CxC Line 37, embryo at physiological maturity

value: embryo at physiological maturity


title: 11178.s1

value: F

tag: site


title: L35_647 environment 2

description: array batch 20202

source_name: CxC Line 35, embryo at physiological maturity


title: HG_CTL2

value: lymphoblast

value: D


title: yFR787_3E10_CTD-S7A_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR787 Rpb1-CTD-S7A cells

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: HG_CTL3

tag: sample id

tag: gender

tag: sentrix id

value: H


title: 11300.s1

value: leukocyte

tag: age at collection (months)


title: yFR682_4E12_bur2D_P-Ser7_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR682 bur2D cells


title: 11345.s1

tag: sentrix position

value: J

value: xm

value: more-than-one-race


title: yFR682_8WG16_bur2D_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR682 bur2D cells

value: 8WG16 (CTD)

value: Abcam


title: yFR682_8WG16_bur2D_CTD_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR682 bur2D cells


title: L30_647 environment 2

description: array batch 20202

tag: population

value: Cayuga x Caledonia, DH

tag: field location

tag: year

source_name: CxC Line 30, embryo at physiological maturity


title: yFR682_3E8_bur2D_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR682 bur2D cells


title: HG_CTL1

source_name: lymphoblast

tag: cell type

value: I

tag: experiment


title: EBSC_CTL20

value: Female

value: L

tag: group


title: yFR682_4E12_bur2D_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR682 bur2D cells


title: 11218.s1

value: Male

tag: family

value: pb

tag: cpea dx

tag: ethnicity

value: white


title: 11004.s1

value: E

tag: distribution

tag: site

value: oi


title: 11584.s1

value: G


title: 11398.s1

value: F


title: yFR682_3E10_bur2D_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR682 bur2D cells

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: EBSC_CTL18

value: leukocyte

tag: sample id

tag: gender

tag: sentrix id

value: K


title: EBSC_CTL19

tag: sentrix position

value: J


title: 11452.s1

value: A

value: kr

tag: age at collection (months)


title: yFR682_3E8_bur2D_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR682 bur2D cells


title: 11378.s1

value: ox

value: asian


title: 11009.s1

value: D


title: L21_647 environment 2

description: array batch 20202

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 21, embryo at physiological maturity

value: embryo at physiological maturity


title: 11054.s1

tag: cell type

value: Male

value: H

tag: experiment

tag: group

tag: family

value: hv

value: white


title: L20_647 environment 2

description: array batch 20556

source_name: CxC Line 20, embryo at physiological maturity


title: L24_647 environment 2

description: array batch 20574

source_name: CxC Line 24, embryo at physiological maturity


title: 11488.s1

value: E

tag: distribution

tag: site

tag: cpea dx

tag: ethnicity

value: more-than-one-race


title: yFR682_3E10_bur2D_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR682 bur2D cells

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: yFR551_8WG16_ctk1D_CTD_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR551 ctk1D cells

value: 8WG16 (CTD)

value: Abcam


title: L19_647 environment 2

description: array batch 20202

source_name: CxC Line 19, embryo at physiological maturity


title: L29_647 environment 2

description: array batch 20202

source_name: CxC Line 29, embryo at physiological maturity


title: 11270.s1.1

value: leukocyte

tag: sample id

tag: gender

tag: sentrix id

tag: sentrix position

value: xm


title: 11216.s1

value: K

value: oi

tag: age at collection (months)


title: yFR551_8WG16_ctk1D_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR551 ctk1D cells


title: L12_647 environment 2

description: array batch 20574

tag: population

value: Cayuga x Caledonia, DH

tag: field location

tag: year

tag: tissue

source_name: CxC Line 12, embryo at physiological maturity


title: L18_647 environment 2

description: array batch 20556

value: Ketola, Cornell University, Ithaca, NY

source_name: CxC Line 18, embryo at physiological maturity


title: 11459.s1

source_name: leukocyte

tag: cell type

value: J

tag: experiment

tag: group

tag: family


title: 11282.s1

value: L

tag: distribution

tag: site

value: kr

tag: cpea dx

tag: ethnicity


title: yFR551_4E12_ctk1D_P-Ser7_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR551 ctk1D cells

tag: strain

tag: antibody

tag: vendor


title: EBSC_CTL17

tag: sample id

tag: gender

value: Female

tag: sentrix id

tag: sentrix position

value: I


title: 11599.s1

value: Male

value: A

tag: age at collection (months)

value: white


title: L10_647 environment 2

description: array batch 20556

tag: population

tag: field location

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 10, embryo at physiological maturity

value: embryo at physiological maturity


title: L11_647 environment 2

description: array batch 20574

source_name: CxC Line 11, embryo at physiological maturity


title: L3_647 environment 2

description: array batch 20202

source_name: Pre-anthesis spike bulk

source_name: CxC Line 3, embryo at physiological maturity


title: 11428.s1.1

tag: cell type

value: D

tag: experiment

tag: group

tag: family

value: more-than-one-race


title: 11230.s1.1

value: leukocyte

value: B

tag: distribution

tag: site

value: fl

tag: cpea dx

tag: ethnicity


title: 11545.s1

tag: sample id

value: F


title: yFR551_4E12_ctk1D_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR551 ctk1D cells

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: yFR551_3E8_ctk1D_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR551 ctk1D cells


title: EBSC_CTL16

tag: gender

tag: sentrix id

tag: sentrix position


title: yFR551_3E10_ctk1D_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR551 ctk1D cells


title: 11522.s1

value: J

value: ox

tag: age at collection (months)


title: 11504.s1

value: E


title: L1_647 environment 2

description: array batch 20556

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

source_name: CxC Line 1, embryo at physiological maturity


title: 11194.s1

tag: cell type

value: Male

tag: experiment

tag: group

tag: family


title: L226_555 environment 2

description: array batch 20202

source_name: CxC Line 226, embryo at physiological maturity


title: 11334.s1

value: G

tag: distribution

tag: site

value: sb

tag: cpea dx

tag: ethnicity


title: yFR487_9E10_rpb1-9xmyc_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy (Rpb1-9myc), using 9E10 antibody, measured by the IP Tag/Ip NoTag ratio,  yFR487 rpb1-9myc/yFR116 Wt cells

tag: strain

tag: antibody

tag: source

value: Alain Verreault

value: Myc 9E10


title: yFR551_3E10_ctk1D_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR551 ctk1D cells

tag: vendor


title: yFR551_3E8_ctk1D_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR551 ctk1D cells


title: 11381.s1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

tag: sample id

tag: gender

tag: sentrix id

tag: sentrix position

value: I

value: kr

tag: age at collection (months)

value: not-specified


title: yFR487_9E10_rpb1-9xmyc_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy (Rpb1-9myc), using 9E10 antibody, measured by the IP Tag/Ip NoTag ratio,  yFR487 rpb1-9myc/yFR116 Wt cells


title: L221_555 environment 2

description: array batch 20556

source_name: CxC Line 221, embryo at physiological maturity

tag: population

tag: field location

tag: year

tag: tissue

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: 11383.s1

tag: cell type

value: leukocyte

tag: experiment

tag: group

tag: family

tag: distribution

value: hv

value: white


title: 11096.s1

tag: site

value: xm

tag: cpea dx

tag: ethnicity


title: 11041.s1

tag: sample id

value: J

value: ox

value: african-amer


title: 11075.s1

tag: gender

value: Male

value: L


title: 11028.s1

tag: sentrix id

value: D

value: sb

value: other


title: L215_555 environment 2

description: array batch 20574

source_name: CxC Line 215, embryo at physiological maturity

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY


title: 11580.s1

tag: sentrix position

value: H


title: yFR117_8WG16_S288C_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR117 S288C Wt cells

tag: strain

tag: antibody

value: 8WG16 (CTD)

tag: vendor

value: Abcam


title: L213_555 environment 2

description: array batch 20202

source_name: CxC Line 213, embryo at physiological maturity

tag: population

tag: field location

tag: year

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: 11251.s1

tag: cell type

value: leukocyte

value: A

tag: experiment

value: fl

tag: age at collection (months)

value: white


title: 11013.s1

tag: group

tag: family

tag: distribution

value: xm


title: yFR117_3E10_S288C_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR117 S288C Wt cells

value: Helmholtz Zentrum


title: L214_555 environment 2

description: array batch 20202

source_name: CxC Line 214, embryo at physiological maturity

tag: tissue


title: yFR117_8WG16_S288C_CTD_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR117 S288C Wt cells


title: yFR117_3E8_S288C_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR117 S288C Wt cells


title: L212_555 environment 2

description: array batch 20202

source_name: CxC Line 212, embryo at physiological maturity


title: 11093.s1

tag: sample id

value: Male

value: G

tag: site

tag: cpea dx

tag: ethnicity


title: EBSC_CTL15

tag: gender

value: Female

tag: sentrix id

tag: sentrix position

value: C


title: L210_555 environment 2

description: array batch 20556

source_name: CxC Line 210, embryo at physiological maturity

tag: population

value: Cayuga x Caledonia, DH


title: L9_647 environment 2

description: array batch 20574

tag: field location

value: Ketola, Cornell University, Ithaca, NY

source_name: CxC Line 9, embryo at physiological maturity


title: L217_555 environment 2

description: array batch 20574

source_name: CxC Line 217, embryo at physiological maturity

tag: year


title: yFR117_3E10_S288C_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR117 S288C Wt cells

tag: strain

tag: antibody

tag: vendor


title: EBSC_CTL13

tag: cell type

tag: experiment

tag: group


title: 11245.s1

value: I

tag: family

tag: distribution

value: kr

tag: age at collection (months)

value: more-than-one-race


title: yFR117_3E8_S288C_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR117 S288C Wt cells


title: EBSC_CTL14

tag: sample id

value: B


title: 11520.s1

value: K

tag: site

tag: cpea dx

tag: ethnicity


title: 11415.s1

value: leukocyte

tag: gender

tag: sentrix id

tag: sentrix position

value: F

value: sb


title: L209_555 environment 2

description: array batch 20574

source_name: CxC Line 209, embryo at physiological maturity

tag: population

tag: field location

tag: year

tag: tissue

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: 11197.s1

tag: cell type

value: H

value: xx

value: white


title: L208_555 environment 2

description: array batch 20202

source_name: CxC Line 208, embryo at physiological maturity


title: 11544.s1

source_name: leukocyte

value: Male

tag: experiment

value: kc

value: other


title: EBSC_CTL12

value: Female

value: L

tag: group


title: yFR116_H5_W303_P-Ser2_Rep4

description: Biological replicate 4 of 4. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells

tag: strain

tag: antibody

value: H5 (Ser2)

tag: vendor

value: Covance


title: L207_555 environment 2

description: array batch 20574

source_name: CxC Line 207, embryo at physiological maturity

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY


title: yFR116_H5_W303_P-Ser2_Rep3

description: Biological replicate 3 of 4. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells


title: EBSC_CTL11

value: leukocyte

tag: sample id

value: K


title: 11031.s1

value: F

tag: family

tag: distribution

tag: site

value: kr

tag: age at collection (months)


title: yFR116_H5_W303_P-Ser2_Rep1

description: Biological replicate 1 of 4. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells


title: L201_555 environment 2

description: array batch 20202

source_name: CxC Line 201, embryo at physiological maturity

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: L205_555 environment 2

description: array batch 20202

source_name: CxC Line 205, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: yFR116_H5_W303_P-Ser2_Rep2

description: Biological replicate 2 of 4. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells


title: yFR116_H14_W303_P-Ser5_Rep4

description: Biological replicate 4 of 4. RNAPII CTD P-Ser5 occupancy, using H14 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells


title: L206_555 environment 2

description: array batch 20574

source_name: CxC Line 206, embryo at physiological maturity


title: 11696.s1

tag: gender

tag: sentrix id

value: J

value: oi

tag: cpea dx

tag: ethnicity


title: 11404.s1

value: Male

tag: sentrix position

value: C

value: xx

value: white


title: 11046.s1

value: D

value: xm


title: L200_555 environment 2

description: array batch 20556

source_name: CxC Line 200, embryo at physiological maturity

tag: population

tag: field location

tag: year

tag: tissue


title: 11199.s1

tag: cell type

value: L

tag: experiment

tag: group

value: fl


title: 11296.s1

tag: sample id

value: sb


title: 11312.s1

value: leukocyte

tag: family

value: kc

value: other


title: yFR116_H14_W303_P-Ser5_Rep1

description: Biological replicate 1 of 4. RNAPII CTD P-Ser5 occupancy, using H14 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells

tag: strain

tag: antibody

tag: vendor

value: Covance


title: L198_555 environment 2

description: array batch 20574

source_name: CxC Line 198, embryo at physiological maturity

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

value: embryo at physiological maturity


title: 11366.s1

tag: gender

value: G

tag: distribution

tag: site

tag: age at collection (months)


title: yFR116_H14_W303_P-Ser5_Rep2

description: Biological replicate 2 of 4. RNAPII CTD P-Ser5 occupancy, using H14 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells


title: EBSC_CTL10

value: Female

tag: sentrix id

tag: sentrix position

value: J


title: 11089.s1

value: Male

value: oi

tag: cpea dx

tag: ethnicity


title: yFR116_H14_W303_P-Ser5_Rep3

description: Biological replicate 3 of 4. RNAPII CTD P-Ser5 occupancy, using H14 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells


title: L196_555 environment 2

description: array batch 20202

source_name: CxC Line 196, embryo at physiological maturity

tag: population

tag: field location

tag: year

tag: tissue

value: Pre-anthesis spike bulk


title: L195_555 environment 2

description: array batch 20202

source_name: CxC Line 195, embryo at physiological maturity


title: L197_555 environment 2

description: array batch 20202

source_name: CxC Line 197, embryo at physiological maturity


title: 11511.s1

tag: cell type

tag: sample id

value: A

tag: experiment

tag: group

value: white


title: 11546.s1

value: K

tag: family


title: 11318.s1

tag: gender

value: xm


title: yFR116_8WG16_W303_CTD_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells

tag: strain

tag: antibody

value: 8WG16 (CTD)

tag: vendor

value: Abcam


title: 11298.s1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

value: leukocyte

tag: sentrix id

value: B

tag: distribution

tag: site

value: sb

tag: age at collection (months)


title: 11441.s1

tag: sentrix position

tag: cpea dx

tag: ethnicity

value: more-than-one-race


title: 11235.s1

value: I


title: yFR116_8WG16_W303_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells


title: L191_555 environment 2

description: array batch 20202

source_name: CxC Line 191, embryo at physiological maturity

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: embryo at physiological maturity


title: L194_555 environment 2

description: array batch 20574

source_name: CxC Line 194, embryo at physiological maturity


title: EBSC_CTL9

tag: cell type

tag: sample id

value: Female

tag: experiment

tag: group


title: 11641.s1

tag: gender

value: Male

value: D

tag: family

value: pb


title: EBSC_CTL8

tag: sentrix id

value: H